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Package ‘meta’

February 5, 2022
Title General Package for Meta-Analysis
Version 5.2-0
Date 2022-02-04
Depends R (>= 4.0.0)
Imports metafor (>= 3.0-0), grid, lme4, CompQuadForm, xml2
Suggests BiasedUrn
Author Guido Schwarzer [cre, aut] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer Guido Schwarzer <[email protected]>

URL https://github.com/guido-s/meta/
https://link.springer.com/book/10.1007/978-3-319-21416-0
Description User-friendly general package providing standard methods for meta-
analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-
0>, ``Meta-Analysis with R'' (2015):
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from 'RevMan 5';
- prediction interval, Hartung-Knapp method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression;
- generalised linear mixed models;
- produce forest plot summarising several (subgroup) meta-analyses.
License GPL (>= 2)
Encoding UTF-8
RoxygenNote 7.1.2
NeedsCompilation no
Repository CRAN
Date/Publication 2022-02-05 01:10:02 UTC

1
2 R topics documented:

R topics documented:
meta-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
amlodipine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
as.data.frame.meta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
baujat.meta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
bubble.metareg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
ci . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
cisapride . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
drapery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Fleiss1993bin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Fleiss1993cont . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
forest.meta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
forest.metabind . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
funnel.meta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
gs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
JAMAlabels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
labbe.metabin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
labels.meta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
longarm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
metabias.meta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
metabias.rm5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
metabin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
metabind . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
metacont . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
metacor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
metacr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
metacum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
metagen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
metainc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
metainf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
metamean . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
metamerge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
metaprop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
metarate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
metareg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
nnt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190
Olkin1995 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
or2smd . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
Pagliaro1992 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
print.meta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
print.rm5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
print.summary.meta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
radial.meta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
read.mtv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206
read.rm5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208
settings.meta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
smd2or . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
meta-package 3

smoking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
summary.meta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
summary.rm5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
trimfill.meta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
update.meta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227
weights.meta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
woodyplants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235

Index 237

meta-package meta: Brief overview of methods and general hints

Description
R package meta is a user-friendly general package providing standard methods for meta-analysis
and supporting Schwarzer et al. (2015), https://link.springer.com/book/10.1007/978-3-319-21416-0.

Details
R package meta (Schwarzer, 2007; Balduzzi et al., 2019) provides the following statistical methods
for meta-analysis.

1. Fixed effect and random effects model:

• Meta-analysis of continuous outcome data (metacont)
• Meta-analysis of binary outcome data (metabin)
• Meta-analysis of incidence rates (metainc)
• Generic inverse variance meta-analysis (metagen)
• Meta-analysis of single correlations (metacor)
• Meta-analysis of single means (metamean)
• Meta-analysis of single proportions (metaprop)
• Meta-analysis of single incidence rates (metarate)
2. Several plots for meta-analysis:
• Forest plot (forest.meta, forest.metabind)
• Funnel plot (funnel.meta)
• Galbraith plot / radial plot (radial.meta)
• L’Abbe plot for meta-analysis with binary outcome data (labbe.metabin, labbe.default)
• Baujat plot to explore heterogeneity in meta-analysis (baujat.meta)
• Bubble plot to display the result of a meta-regression (bubble.metareg)
3. Statistical tests for funnel plot asymmetry (metabias.meta, metabias.rm5) and trim-and-fill
method (trimfill.meta, trimfill.default) to evaluate bias in meta-analysis
4. Cumulative meta-analysis (metacum) and leave-one-out meta-analysis (metainf)
5. Meta-regression (metareg)
4 meta-package

6. Import data from Review Manager 5 (read.rm5); see also metacr to conduct meta-analysis
for a single comparison and outcome from a Cochrane review
7. Prediction interval for the treatment effect of a new study (Higgins et al., 2009); see argument
prediction in meta-analysis functions, e.g., metagen
8. Hartung-Knapp method for random effects meta-analysis (Hartung & Knapp, 2001a,b); see
argument hakn in meta-analysis functions, e.g., metagen
9. Various estimators for the between-study variance τ 2 in a random effects model (Veroniki et
al., 2016); see argument method.tau in meta-analysis functions, e.g., metagen
10. Generalised linear mixed models (metabin, metainc, metaprop, and metarate)

The following more advanced statistical methods are provided by add-on R packages:

• Frequentist methods for network meta-analysis (R package netmeta)

• Advanced methods to model and adjust for bias in meta-analysis (R package metasens)

Results of several meta-analyses can be combined with metabind. This is, for example, useful to
generate a forest plot with results of subgroup analyses.
See settings.meta to learn how to print and specify default meta-analysis methods used during
your R session. For example, the function can be used to specify general settings:

• settings.meta("revman5")
• settings.meta("jama")
• settings.meta("iqwig5")
• settings.meta("iqwig6")
• settings.meta("geneexpr")

The first command can be used to reproduce meta-analyses from Cochrane reviews conducted with
Review Manager 5 (RevMan 5, https://training.cochrane.org/online-learning/core-software-cochrane-revie
revman) and specifies to use a RevMan 5 layout in forest plots.
The second command can be used to generate forest plots following instructions for authors of
the Journal of the American Medical Association (https://jamanetwork.com/journals/jama/
pages/instructions-for-authors/). Study labels according to JAMA guidelines can be gener-
ated using labels.meta.
The next two commands implement the recommendations of the Institute for Quality and Efficiency
in Health Care (IQWiG), Germany accordinging to General Methods 5 and 6, respectively (https:
//www.iqwig.de/en/about-us/methods/methods-paper/).
The last setting can be used to print p-values in scientific notation and to suppress the calculation of
confidence intervals for the between-study variance.
In addition, settings.meta can be used to change individual settings. For example, the following
R command specifies the use of the Hartung-Knapp and Paule-Mandel methods, and the printing of
prediction intervals in the current R session for any meta-analysis generated after execution of this
command:

• settings.meta(hakn=TRUE,method.tau="PM",prediction=TRUE)
meta-package 5

Type help(package = "meta") for a listing of R functions and datasets available in meta.
Balduzzi et al. (2019) is the preferred citation in publications for meta. Type citation("meta")
for a BibTeX entry of this publication.
To report problems and bugs

• type bug.report(package = "meta") if you do not use RStudio,

• send an email to Guido Schwarzer <[email protected]> if you use RStudio.

The development version of meta is available on GitHub https://github.com/guido-s/meta/.

Note

R package meta imports R functions from metafor (Viechtbauer, 2010) to

• estimate the between-study variance τ 2 ,

• conduct meta-regression,
• estimate generalised linear mixed models.

Author(s)

Guido Schwarzer <[email protected]>

References

Balduzzi S, Rücker G, Schwarzer G (2019): How to perform a meta-analysis with R: a practical

tutorial. Evidence-Based Mental Health, 22, 153–160
Hartung J, Knapp G (2001a): On tests of the overall treatment effect in meta-analysis with normally
distributed responses. Statistics in Medicine, 20, 1771–82
Hartung J, Knapp G (2001b): A refined method for the meta-analysis of controlled clinical trials
with binary outcome. Statistics in Medicine, 20, 3875–89
Higgins JPT, Thompson SG, Spiegelhalter DJ (2009): A re-evaluation of random-effects meta-
analysis. Journal of the Royal Statistical Society: Series A, 172, 137–59
Schwarzer G (2007): meta: An R package for meta-analysis. R News, 7, 40–5
Schwarzer G, Carpenter JR and Rücker G (2015): Meta-Analysis with R (Use-R!). Springer Inter-
national Publishing, Switzerland
Veroniki AA, Jackson D, Viechtbauer W, Bender R, Bowden J, Knapp G, et al. (2016): Methods
to estimate the between-study variance and its uncertainty in meta-analysis. Research Synthesis
Methods, 7, 55–79
Viechtbauer W (2010): Conducting Meta-Analyses in R with the metafor Package. Journal of
Statistical Software, 36, 1–48
6 amlodipine

amlodipine Amlodipine for Work Capacity

Description
Meta-analysis on the effect of amlodipine on work capacity.
This meta-analysis is used as a data example in Hartung and Knapp (2001).

Format
A data frame with the following columns:

study study label

n.amlo number of observations in amlodipine group
mean.amlo estimated mean in amlodipine group
var.amlo variance in amlodipine group
n.plac number of observations in placebo group
mean.plac estimated mean in placebo group
var.plac variance in placebo group

Source
Hartung J & Knapp G (2001): On tests of the overall treatment effect in meta-analysis with normally
distributed responses. Statistics in Medicine, 20, 1771–82

m <- metacont(n.amlo, mean.amlo, sqrt(var.amlo), n.plac, mean.plac, sqrt(var.plac),

data = amlodipine, studlab = study)
m.hakn <- update(m, hakn = TRUE)

# Same results for mean difference as in Table III in Hartung and

# Knapp (2001)
#
vars.fixed <- c("TE.fixed", "lower.fixed", "upper.fixed")
vars.random <- c("TE.random", "lower.random", "upper.random")
#
res.fixed <- as.data.frame(m[vars.fixed])
names(res.fixed) <- vars.random
#
res.md <- rbind(res.fixed,
as.data.frame(m[vars.random]),
as.data.frame.meta 7

as.data.frame(m.hakn[vars.random]))
#
res.md <- round(res.md, 5)
#
row.names(res.md) <- c("FE", "RE", "RE (HaKn)")
names(res.md) <- c("Absolute difference", "CI lower", "CI upper")
#
res.md

as.data.frame.meta Additional functions for objects of class meta

Description

The as.data.frame method returns a data frame containing information on individual studies, e.g.,
estimated treatment effect and its standard error.

Usage

## S3 method for class 'meta'

as.data.frame(x, row.names = NULL, optional = FALSE, ...)

Arguments

x An object of class meta.

row.names NULL or a character vector giving the row names for the data frame.
optional logical. If TRUE, setting row names and converting column names (to syntactic
names) is optional.
... other arguments

Value

A data frame is returned by the function as.data.frame.

Author(s)

Guido Schwarzer <[email protected]>

See Also

metabin, metacont, metagen, forest.meta

8 baujat.meta

Examples
data(Fleiss1993cont)
#
# Generate additional variable with grouping information
#
Fleiss1993cont$group <- c(1, 2, 1, 1, 2)
#
# Do meta-analysis without grouping information
#
m1 <- metacont(n.psyc, mean.psyc, sd.psyc, n.cont, mean.cont, sd.cont,
data = Fleiss1993cont, sm = "SMD", studlab = paste(study, year))
#
# Update meta-analysis object and do subgroup analyses
#
update(m1, subgroup = group)

# Same result using metacont function directly

#
m2 <- metacont(n.psyc, mean.psyc, sd.psyc, n.cont, mean.cont, sd.cont,
data = Fleiss1993cont, sm = "SMD", studlab = paste(study, year),
subgroup = group)
m2

# Compare printout of the following two commands

#
as.data.frame(m1)
m1$data

baujat.meta Baujat plot to explore heterogeneity in meta-analysis

Description
Draw a Baujat plot to explore heterogeneity in meta-analysis.

Usage
## S3 method for class 'meta'
baujat(
x,
yscale = 1,
xlim,
ylim,
xlab = "Contribution to overall heterogeneity",
ylab = "Influence on overall result",
pch = 21,
cex = 1,
col = "black",
baujat.meta 9

bg = "darkgray",
studlab = TRUE,
cex.studlab = 0.8,
pos.studlab = 2,
offset = 0.5,
xmin = 0,
ymin = 0,
grid = TRUE,
col.grid = "lightgray",
lty.grid = "dotted",
lwd.grid = par("lwd"),
pty = "s",
...
)

Arguments
x An object of class meta.
yscale Scaling factor for values on y-axis.
xlim The x limits (min,max) of the plot.
ylim The y limits (min,max) of the plot.
xlab A label for the x-axis.
ylab A label for the y-axis.
pch The plotting symbol used for individual studies.
cex The magnification to be used for plotting symbol.
col A vector with colour of plotting symbols.
bg A vector with background colour of plotting symbols (only used if pch in 21:25).
studlab A logical indicating whether study labels should be printed in the graph. A
vector with study labels can also be provided (must be of same length as x$TE
then).
cex.studlab The magnification for study labels.
pos.studlab Position of study labels, see argument pos in text.
offset Offset for study labels (see text).
xmin A numeric specifying minimal value to print study labels (on x-axis).
ymin A numeric specifying minimal value to print study labels (on y-axis).
grid A logical indicating whether a grid is printed in the plot.
col.grid Colour for grid lines.
lty.grid The line type for grid lines.
lwd.grid The line width for grid lines.
pty A character specifying type of plot region (see par).
... Graphical arguments as in par may also be passed as arguments.
10 baujat.meta

Details
Baujat et al. (2002) introduced a scatter plot to explore heterogeneity in meta-analysis. On the
x-axis the contribution of each study to the overall heterogeneity statistic (see list object Q of the
meta-analysis object x) is plotted. On the y-axis the standardised difference of the overall treatment
effect with and without each study is plotted; this quantity describes the influence of each study on
the overal treatment effect.
Internally, the metainf function is used to calculate the values on the y-axis.

Value
A data.frame with the following variables:

x Coordinate on x-axis (contribution to heterogeneity statistic)

y Coordinate on y-axis (influence on overall treatment effect)

Author(s)
Guido Schwarzer <[email protected]>

References
Baujat B, Mahé C, Pignon JP, Hill C (2002): A graphical method for exploring heterogeneity in
meta-analyses: Application to a meta-analysis of 65 trials. Statistics in Medicine, 30, 2641–52

m1 <- metabin(ev.exp, n.exp, ev.cont, n.cont,

data = Olkin1995, sm = "OR", method = "I", studlab = paste(author, year))

# Generate Baujat plot

baujat(m1)

## Not run:
# Do not print study labels if the x-value is smaller than 4 and
# the y-value is smaller than 1
baujat(m1, yscale = 10, xmin = 4, ymin = 1)

# Change position of study labels

baujat(m1, yscale = 10, xmin = 4, ymin = 1,
pos = 1, xlim = c(0, 6.5))

# Generate Baujat plot and assign x- and y- coordinates to R object

# b1
b1 <- baujat(m1)
bubble.metareg 11

# Calculate overall heterogeneity statistic

sum(b1$x)
m1$Q

## End(Not run)

bubble.metareg Bubble plot to display the result of a meta-regression

Description
Draw a bubble plot to display the result of a meta-regression.

Usage
## S3 method for class 'metareg'
bubble(
x,
xlim,
ylim,
xlab,
ylab,
cex,
min.cex = 0.5,
max.cex = 5,
pch = 21,
col = "black",
bg = "darkgray",
lty = 1,
lwd = 1,
col.line = "black",
studlab = FALSE,
cex.studlab = 0.8,
pos.studlab = 2,
offset = 0.5,
regline = TRUE,
backtransf = x$.meta$x$backtransf,
ref,
col.ref = "lightgray",
lty.ref = 1,
lwd.ref = 1,
axes = TRUE,
box = TRUE,
...
)

bubble(x, ...)
12 bubble.metareg

Arguments

x An object of class metareg.

xlim The x limits (min,max) of the plot.
ylim The y limits (min,max) of the plot.
xlab A label for the x-axis.
ylab A label for the y-axis.
cex The magnification to be used for plotting symbols.
min.cex Minimal magnification for plotting symbols.
max.cex Maximal magnification for plotting symbols.
pch The plotting symbol used for individual studies.
col A vector with colour of plotting symbols.
bg A vector with background colour of plotting symbols (only used if pch in 21:25).
lty The line type for the meta-regression line.
lwd The line width for the meta-regression line.
col.line Colour for the meta-regression line.
studlab A logical indicating whether study labels should be printed in the graph. A
vector with study labels can also be provided (must be of same length as the
numer of studies in the meta-analysis then).
cex.studlab The magnification for study labels.
pos.studlab Position of study labels, see argument pos in text.
offset Offset for study labels (see text).
regline A logical indicating whether a regression line should be added to the bubble
plot.
backtransf A logical indicating whether results for relative summary measures (argument
sm equal to "OR", "RR", "HR", or "IRR") should be back transformed. If backtransf=TRUE,
results for sm="OR" are printed as odds ratios rather than log odds ratios, for ex-
ample.
ref A numerical giving the reference value to be plotted as a line in the bubble plot.
No reference line is plotted if argument ref is equal to NA.
col.ref Colour of the reference line.
lty.ref The line type for the reference line.
lwd.ref The line width for the reference line.
axes A logical indicating whether axes should be printed.
box A logical indicating whether a box should be printed.
... Graphical arguments as in par may also be passed as arguments.
bubble.metareg 13

Details
A bubble plot can be used to display the result of a meta-regression. It is a scatter plot with the
treatment effect for each study on the y-axis and the covariate used in the meta-regression on the
x-axis. Typically, the size of the plotting symbol is inversely proportional to the variance of the
estimated treatment effect (Thompson & Higgins, 2002).
Argument cex specifies the plotting size for each individual study. If this argument is missing the
weights from the meta-regression model will be used (which typically is a random effects model).
Use cex="fixed" in order to utilise weights from a fixed effect model to define the size of the
plotted symbols (even for a random effects meta-regression). If a vector with individual study
weights is provided, the length of this vector must be of the same length as the number of studies.
Arguments min.cex and max.cex can be used to define the size of the smallest and largest plotting
symbol. The plotting size of the most precise study is set to max.cex whereas the plotting size of
all studies with a plotting size smaller than min.cex will be set to min.cex.
For a meta-regression with more than one covariate. Only a scatter plot of the first covariate in the
regression model is shown. In this case the effect of the first covariate adjusted for other covariates
in the meta-regression model is shown.
For a factor or categorial covariate separate bubble plots for each group compared to the baseline
group are plotted.

Author(s)
Guido Schwarzer <[email protected]>

References
Thompson SG, Higgins JP (2002): How should meta-regression analyses be undertaken and inter-
preted? Statistics in Medicine, 21, 1559–73

# Add some (fictitious) grouping variables:

Fleiss1993cont$age <- c(55, 65, 52, 65, 58)
Fleiss1993cont$region <- c("Europe", "Europe", "Asia", "Asia", "Europe")

m1 <- metacont(n.psyc, mean.psyc, sd.psyc, n.cont, mean.cont, sd.cont,

data = Fleiss1993cont, sm = "MD")

mr1 <- metareg(m1, region)

mr1

bubble(mr1)
bubble(mr1, lwd = 2, col.line = "blue")
14 ci

mr2 <- metareg(m1, age)

mr2

bubble(mr2, lwd = 2, col.line = "blue", xlim = c(50, 70))

bubble(mr2, lwd = 2, col.line = "blue", xlim = c(50, 70), cex = "fixed")

# Do not print regression line

#
bubble(mr2, lwd = 2, col.line = "blue", xlim = c(50, 70), regline = FALSE)

ci Calculation of confidence intervals (based on normal approximation

or t-distribution)

Description
Calculation of confidence intervals; based on normal approximation or t-distribution.

Usage
ci(TE, seTE, level = 0.95, df = NULL, null.effect = 0)

Arguments
TE Estimated treatment effect.
seTE Standard error of treatment estimate.
level The confidence level required.
df Degrees of freedom (for confidence intervals based on t-distribution).
null.effect A numeric value specifying the effect under the null hypothesis.

Value
List with components

TE Estimated treatment effect

seTE Standard error of treatment estimate
lower Lower confidence limits
upper Upper confidence limits
statistic Test statistic (either z-score or t-score)
p P-value of text.with null hypothesis TE=0
level The confidence level required
df Degrees of freedom (t-distribution)
cisapride 15

Note
This function is primarily called from other functions of the library meta, e.g. forest.meta,
summary.meta.

Author(s)
Guido Schwarzer <[email protected]>

Examples
data.frame(ci(170, 10))
data.frame(ci(170, 10, 0.99))
data.frame(ci(1.959964, 1))
data.frame(ci(2.2621571628, 1, df = 9))

cisapride Cisapride in Non-Ulcer Dispepsia

Description
Meta-analysis on cisapride in non-ulcer dispepsia.
This meta-analysis is used as a data example in Hartung and Knapp (2001).

Format
A data frame with the following columns:

study study label

event.cisa number of events in cisapride group
n.cisa number of observations in cisapride group
event.plac number of events in placebo group
n.plac number of observations in placebo group

Source
Hartung J & Knapp G (2001): A refined method for the meta-analysis of controlled clinical trials
with binary outcome. Statistics in Medicine, 20, 3875–89

m.or <- metabin(event.cisa, n.cisa, event.plac, n.plac,

16 drapery

data = cisapride, sm = "OR", method = "Inverse",

studlab = study, addincr = TRUE)

m.or.hakn <- update(m.or, hakn = TRUE)

m.rr <- update(m.or, sm = "RR")
m.rr.hakn <- update(m.or, sm = "RR", hakn = TRUE)

vars.fixed <- c("TE.fixed", "lower.fixed", "upper.fixed")

vars.random <- c("TE.random", "lower.random", "upper.random")
#
res.fixed.or <- as.data.frame(m.or[vars.fixed])
names(res.fixed.or) <- vars.random
#
res.fixed.rr <- as.data.frame(m.rr[vars.fixed])
names(res.fixed.rr) <- vars.random

# Results for log risk ratio - see Table VII in Hartung and Knapp (2001)
#
res.rr <- rbind(res.fixed.rr,
as.data.frame(m.rr[vars.random]),
as.data.frame(m.rr.hakn[vars.random]))
#
row.names(res.rr) <- c("FE", "RE", "RE (HaKn)")
names(res.rr) <- c("Log risk ratio", "CI lower", "CI upper")
#
res.rr

# Results for log odds ratio (Table VII in Hartung and Knapp 2001)
#
res.or <- rbind(res.fixed.or,
as.data.frame(m.or[vars.random]),
as.data.frame(m.or.hakn[vars.random]))
#
row.names(res.or) <- c("FE", "RE", "RE (HaKn)")
names(res.or) <- c("Log odds ratio", "CI lower", "CI upper")
#
res.or

drapery Drapery plot

Description
Draw a drapery plot with (scaled) p-value curves for individual studies and meta-analysis estimates.

Usage
drapery(
x,
drapery 17

type = "zvalue",
layout = "grayscale",
study.results = TRUE,
lty.study = 1,
lwd.study = 1,
col.study = "darkgray",
labels,
col.labels = "black",
cex.labels = 0.7,
subset.labels,
srt.labels,
fixed = x$fixed,
random = x$random,
lty.fixed = 1,
lwd.fixed = max(3, lwd.study),
col.fixed = "blue",
lty.random = 1,
lwd.random = lwd.fixed,
col.random = "red",
sign = NULL,
lty.sign = 1,
lwd.sign = 1,
col.sign = "black",
prediction = random,
col.predict = "lightblue",
alpha = if (type == "zvalue") c(0.001, 0.01, 0.05, 0.1) else c(0.01, 0.05, 0.1),
lty.alpha = 2,
lwd.alpha = 1,
col.alpha = "black",
cex.alpha = 0.7,
col.null.effect = "black",
legend = TRUE,
pos.legend = "topleft",
bg = "white",
bty = "o",
backtransf = x$backtransf,
xlab,
ylab,
xlim,
ylim,
lwd.max = 2.5,
lwd.study.weight = if (random) "random" else "fixed",
at = NULL,
n.grid = if (type == "zvalue") 10000 else 1000,
mar = c(5.1, 4.1, 4.1, 4.1),
plot = TRUE,
...
)
18 drapery

Arguments
x An object of class meta.
type A character string indicating whether to plot test statistics ("zvalue") or p-
values ("pvalue"), can be abbreviated.
layout A character string for the line layout of individual studies: "grayscale", "equal",
or "linewidth" (see Details), can be abbreviated.
study.results A logical indicating whether results for individual studies should be shown in
the figure.
lty.study Line type for individual studies.
lwd.study Line width for individual studies.
col.study Colour of lines for individual studies.
labels A logical or character string indicating whether study labels should be shown at
the top of the drapery plot; either FALSE, "id", or "studlab"; see Details.
col.labels Colour of study labels.
cex.labels The magnification for study labels.
subset.labels A vector specifying which study labels should be shown in the drapery plot.
srt.labels A numerical vector or single numeric (between 0 and 90) specifying the angle
to rotate study labels; see Details.
fixed A logical indicating whether to show result for the fixed effect / common effect
model.
random A logical indicating whether to show result for the random effects model.
lty.fixed Line type for fixed effect meta-analysis.
lwd.fixed Line width for fixed effect meta-analysis.
col.fixed Colour of lines for fixed effect meta-analysis.
lty.random Line type for random effects meta-analysis.
lwd.random Line width for random effects meta-analysis.
col.random Colour of lines for random effects meta-analysis.
sign Significance level used to highlight significant values in curves.
lty.sign Line type for significant values.
lwd.sign Line width for significant values.
col.sign Line colour for significant values.
prediction A logical indicating whether to show prediction region.
col.predict Colour of prediction region
alpha Horizonal lines are printed for the specified alpha values.
lty.alpha Line type of horizonal lines for alpha values.
lwd.alpha Line width of horizonal lines for alpha values.
col.alpha Colour of horizonal lines for alpha values.
cex.alpha The magnification for the text of the alpha
drapery 19

col.null.effect
Colour of vertical line indicating null effect.
legend A logical indicating whether a legend should be printed.
pos.legend A character string with position of legend (see legend).
bg Background colour of legend (see legend).
bty Type of the box around the legend; either "o" or "n" (see legend).
backtransf A logical indicating whether results should be back transformed on the x-axis.
For example, if backtransf = FALSE, log odds ratios instead of odds ratios are
shown on the x-axis.
xlab A label for the x-axis.
ylab A label for the y-axis.
xlim The x limits (min, max) of the plot.
ylim The y limits (min, max) of the plot (ignored if type = "pvalue").
lwd.max The maximum line width (only considered if argument layout is equal to "linewidth").
lwd.study.weight
A character string indicating whether to determine line width for individual
studies using weights from fixed effect ("fixed") or random effects model
("random"), can be abbreviated (only considered if argument layout is equal to
"linewidth").
at Points at which tick-marks are to be drawn on the x-axis.
n.grid The number of grid points to calculate the p-value or test statistic functions.
mar Physical plot margin, see par.
plot A logical indicating whether to generate a figure.
... Graphical arguments as in par may also be passed as arguments.

Details
The concept of a p-value function, also called confidence curve, goes back to Birnbaum (1961).
A drapery plot, showing p-value functions (or a scaled version based on the corresponding test
statistics) for individual studies as well as meta-analysis estimates, is drawn in the active graphics
window. Furthermore, a prediction region for a single future study is shown as a shaded area. In
contrast to a forest plot, a drapery plot does not provide information for a single confidence level
however for any confidence level.
Argument type can be used to either show p-value functions (Birnbaum, 1961) or a scaled version
(Infanger, 2019) with test statistics (default).
Argument layout determines how curves for individual studies are presented:
• darker gray tones with increasing precision (layout = "grayscale")
• thicker lines with increasing precision (layout = "linewidth")
• equal lines (layout = "equal")
Argument labels determines how curves of individual studies are labelled:
• number of the study in the (unsorted) forest plot / printout of a meta-analysis (labels = "id")
20 drapery

• study labels provided by argument studlab in meta-analysis functions (labels = "studlab")

• no study labels (labels = FALSE)

By default, study labels are used (labels = "studlab") if no label has more than three characters;
otherwise IDs are used (labels = "id"). The connection between IDs and study labels (among
other information) is part of a data frame which is invisibly returned (if argument study.results
= TRUE).
Argument srt.labels can be used to change the rotation of IDs or study labels. By default,
study labels are rotated by +/- 45 degrees if at least one study label has more than three characters;
otherwise labels are not rotated.
If labels = "studlab", labels are rotated by -45 degrees for studies with a treatment estimate
below the fixed effect estimate and otherwise by 45 degrees.

Author(s)
Gerta Rücker <[email protected]>, Guido Schwarzer <[email protected]>

References
Birnbaum A (1961): Confidence Curves: An Omnibus Technique for Estimation and Testing Sta-
tistical Hypotheses. Journal of the American Statistical Association, 56, 246–9
Infanger D and Schmidt-Trucksäss A (2019): P value functions: An underused method to present
research results and to promote quantitative reasoning Statistics in Medicine, 38, 4189–97

# For studies with a significant effect (p < 0.05), show

Fleiss1993cont 21

# study labels and print labels and lines in red

#
drapery(m2,
labels = "studlab", subset.labels = pval < 0.05,
srt.labels = 0, col.labels = "red",
col.study = ifelse(pval < 0.05, "red", "darkgray"))

## End(Not run)

Fleiss1993bin Aspirin after Myocardial Infarction

Description
Meta-analysis on aspirin in preventing death after myocardial infarction.
Data example in Fleiss (1993) for meta-analysis with binary outcomes.

Format
A data frame with the following columns:

study study label

year year of publication
d.asp number of deaths in aspirin group
n.asp number of observations in aspirin group
d.plac number of deaths in placebo group
n.plac number of observations in placebo group

Source
Fleiss JL (1993): The statistical basis of meta-analysis. Statistical Methods in Medical Research, 2,
121–45

Examples
data(Fleiss1993bin)
metabin(d.asp, n.asp, d.plac, n.plac, data = Fleiss1993bin,
studlab = paste(study, year), sm = "OR", random = FALSE)

Fleiss1993cont Mental Health Treatment

Description
Meta-analysis on the Effect of Mental Health Treatment on Medical Utilisation.
Data example in Fleiss (1993) for meta-analysis with continuous outcomes.
22 forest.meta

Format
A data frame with the following columns:

study study label

year year of publication
n.psyc number of observations in psychotherapy group
mean.psyc estimated mean in psychotherapy group
sd.psyc standard deviation in psychotherapy group
n.cont number of observations in control group
mean.cont estimated mean in control group
sd.cont standard deviation in control group

Source
Fleiss JL (1993): The statistical basis of meta-analysis. Statistical Methods in Medical Research, 2,
121–45

forest.meta Forest plot to display the result of a meta-analysis

Description
Draws a forest plot in the active graphics window (using grid graphics system).

Usage
## S3 method for class 'meta'
forest(
x,
sortvar,
studlab = TRUE,
layout = gs("layout"),
fixed = x$fixed,
random = x$random,
overall = x$overall,
text.fixed = x$text.fixed,
forest.meta 23

text.random = x$text.random,
lty.fixed = 2,
lty.random = 3,
col.fixed = "black",
col.random = "black",
text.w.fixed = x$text.w.fixed,
text.w.random = x$text.w.random,
prediction = x$prediction,
text.predict = x$text.predict,
subgroup = TRUE,
subgroup.hetstat = subgroup & (is.character(hetstat) || hetstat),
print.subgroup.labels = TRUE,
subgroup.name = x$subgroup.name,
print.subgroup.name = x$print.subgroup.name,
sep.subgroup = x$sep.subgroup,
text.fixed.w = text.fixed,
text.random.w = text.random,
text.predict.w = text.predict,
bysort = FALSE,
pooled.totals = fixed | random,
pooled.events = FALSE,
pooled.times = FALSE,
study.results = TRUE,
xlab = "",
xlab.pos,
smlab = NULL,
smlab.pos,
xlim = "symmetric",
allstudies = TRUE,
weight.study = NULL,
weight.subgroup,
pscale = x$pscale,
irscale = x$irscale,
irunit = x$irunit,
ref = ifelse(backtransf & is.relative.effect(x$sm), 1, 0),
lower.equi = NA,
upper.equi = NA,
lty.equi = 1,
col.equi = "blue",
fill.equi = "transparent",
leftcols = NULL,
rightcols = NULL,
leftlabs = NULL,
rightlabs = NULL,
label.e = x$label.e,
label.c = x$label.c,
label.e.attach = NULL,
label.c.attach = NULL,
24 forest.meta

label.right = x$label.right,
label.left = x$label.left,
bottom.lr = TRUE,
lab.NA = ".",
lab.NA.effect = "",
lab.NA.weight = "--",
lwd = 1,
at = NULL,
label = TRUE,
type.study = "square",
type.fixed = "diamond",
type.random = type.fixed,
type.subgroup = ifelse(study.results, "diamond", "square"),
type.subgroup.fixed = type.subgroup,
type.subgroup.random = type.subgroup,
col.study = "black",
col.square = "gray",
col.square.lines = col.square,
col.inside = "white",
col.inside.fixed = col.inside,
col.inside.random = col.inside,
col.diamond = "gray",
col.diamond.fixed = col.diamond,
col.diamond.random = col.diamond,
col.diamond.lines = "black",
col.diamond.lines.fixed = col.diamond.lines,
col.diamond.lines.random = col.diamond.lines,
col.predict = "red",
col.predict.lines = "black",
col.by = "darkgray",
col.label.right = "black",
col.label.left = "black",
hetstat = fixed | random | overall.hetstat,
overall.hetstat = x$overall.hetstat,
hetlab = "Heterogeneity: ",
resid.hetstat,
resid.hetlab = "Residual heterogeneity: ",
print.I2,
print.I2.ci = FALSE,
print.tau2,
print.tau2.ci = FALSE,
print.tau = FALSE,
print.tau.ci = FALSE,
print.Q = FALSE,
print.pval.Q,
print.Rb = FALSE,
print.Rb.ci = FALSE,
text.subgroup.nohet = "not applicable",
forest.meta 25

LRT = FALSE,
test.overall = gs("test.overall"),
test.overall.fixed = fixed & overall & test.overall,
test.overall.random = random & overall & test.overall,
label.test.overall.fixed,
label.test.overall.random,
print.stat = TRUE,
test.subgroup = x$test.subgroup,
test.subgroup.fixed = test.subgroup & fixed,
test.subgroup.random = test.subgroup & random,
prediction.subgroup = x$prediction.subgroup,
print.Q.subgroup = TRUE,
label.test.subgroup.fixed,
label.test.subgroup.random,
test.effect.subgroup = gs("test.effect.subgroup"),
test.effect.subgroup.fixed,
test.effect.subgroup.random,
label.test.effect.subgroup.fixed,
label.test.effect.subgroup.random,
text.addline1,
text.addline2,
fontsize = 12,
fontfamily = NULL,
fs.heading = fontsize,
fs.fixed,
fs.random,
fs.predict,
fs.fixed.labels,
fs.random.labels,
fs.predict.labels,
fs.study = fontsize,
fs.study.labels = fs.study,
fs.hetstat,
fs.test.overall,
fs.test.subgroup,
fs.test.effect.subgroup,
fs.addline,
fs.axis = fontsize,
fs.smlab = fontsize,
fs.xlab = fontsize,
fs.lr = fontsize,
ff.heading = "bold",
ff.fixed,
ff.random,
ff.predict,
ff.fixed.labels,
ff.random.labels,
ff.predict.labels,
26 forest.meta

ff.study = "plain",
ff.study.labels = ff.study,
ff.hetstat,
ff.test.overall,
ff.test.subgroup,
ff.test.effect.subgroup,
ff.addline,
ff.axis = "plain",
ff.smlab = "bold",
ff.xlab = "plain",
ff.lr = "plain",
squaresize = 0.8/spacing,
plotwidth = if (layout == "JAMA") "8cm" else "6cm",
colgap = "2mm",
colgap.left = colgap,
colgap.right = colgap,
colgap.studlab = colgap.left,
colgap.forest = colgap,
colgap.forest.left = colgap.forest,
colgap.forest.right = colgap.forest,
calcwidth.pooled = (fixed | random) & (overall | !is.null(x$subgroup)),
calcwidth.fixed = calcwidth.pooled,
calcwidth.random = calcwidth.pooled,
calcwidth.predict = FALSE,
calcwidth.hetstat = FALSE,
calcwidth.tests = FALSE,
calcwidth.subgroup = FALSE,
calcwidth.addline = FALSE,
just = if (layout == "JAMA") "left" else "right",
just.studlab = "left",
just.addcols = "center",
just.addcols.left = just.addcols,
just.addcols.right = just.addcols,
spacing = 1,
addrow,
addrow.overall,
addrow.subgroups,
addrows.below.overall = 0,
new = TRUE,
backtransf = x$backtransf,
digits = gs("digits.forest"),
digits.se = gs("digits.se"),
digits.stat = gs("digits.stat"),
digits.pval = max(gs("digits.pval") - 2, 2),
digits.pval.Q = max(gs("digits.pval.Q") - 2, 2),
digits.Q = gs("digits.Q"),
digits.tau2 = gs("digits.tau2"),
digits.tau = gs("digits.tau"),
forest.meta 27

digits.I2 = max(gs("digits.I2") - 1, 0),

digits.weight = gs("digits.weight"),
digits.mean = digits,
digits.sd = digits.se,
digits.cor = digits,
digits.time = digits,
digits.addcols = digits,
digits.addcols.right = digits.addcols,
digits.addcols.left = digits.addcols,
scientific.pval = gs("scientific.pval"),
big.mark = gs("big.mark"),
zero.pval = if (layout == "JAMA") FALSE else gs("zero.pval"),
JAMA.pval = if (layout == "JAMA") TRUE else gs("JAMA.pval"),
...
)

Arguments
x An object of class meta.
sortvar An optional vector used to sort the individual studies (must be of same length as
x$TE).
studlab A logical indicating whether study labels should be printed in the graph. A
vector with study labels can also be provided (must be of same length as x$TE
then).
layout A character string specifying the layout of the forest plot (see Details).
fixed A logical indicating whether fixed effect / common effect estimate should be
plotted.
random A logical indicating whether random effects estimate should be plotted.
overall A logical indicating whether overall summaries should be plotted. This argu-
ment is useful in a meta-analysis with subgroups if summaries should only be
plotted on group level.
text.fixed A character string used in the plot to label the pooled fixed effect estimate.
text.random A character string used in the plot to label the pooled random effects estimate.
lty.fixed Line type (pooled fixed effect estimate).
lty.random Line type (pooled random effects estimate).
col.fixed Line colour (pooled fixed effect estimate).
col.random Line colour (pooled random effects estimate).
text.w.fixed A character string used to label weights of fixed effect model.
text.w.random A character string used to label weights of random effects model.
prediction A logical indicating whether a prediction interval should be printed.
text.predict A character string used in the plot to label the prediction interval.
subgroup A single logical or logical vector indicating whether / which subgroup results
should be shown in forest plot. This argument is useful in a meta-analysis with
subgroups if summaries should not be plotted for (some) subgroups.
28 forest.meta

subgroup.hetstat
A single logical or logical vector indicating whether / which information on
heterogeneity in subgroups should be shown in forest plot. This argument is
useful in a meta-analysis with subgroups if heterogeneity statistics should not
be printed for (some) subgroups.
print.subgroup.labels
A logical indicating whether subgroup label should be printed.
subgroup.name A character string with a label for the grouping variable.
print.subgroup.name
A logical indicating whether the name of the grouping variable should be printed
in front of the group labels.
sep.subgroup A character string defining the separator between label and levels of grouping
variable.
text.fixed.w A character string to label the pooled fixed effect estimate within subgroups, or
a character vector of same length as number of subgroups with corresponging
labels.
text.random.w A character string to label the pooled random effect estimate within subgroups,
or a character vector of same length as number of subgroups with corresponging
labels.
text.predict.w A character string to label the prediction interval within subgroups, or a charac-
ter vector of same length as number of subgroups with corresponging labels.
bysort A logical indicating whether groups should be ordered alphabetically.
pooled.totals A logical indicating whether total number of observations should be given in the
figure.
pooled.events A logical indicating whether total number of events should be given in the figure.
pooled.times A logical indicating whether total person time at risk should be given in the
figure.
study.results A logical indicating whether results for individual studies should be shown in
the figure (useful to only plot subgroup results).
xlab A label for the x-axis.
xlab.pos A numeric specifying the center of the label on the x-axis.
smlab A label for the summary measure (printed at top of figure).
smlab.pos A numeric specifying the center of the label for the summary measure.
xlim The x limits (min,max) of the plot, or the character "s" to produce symmetric
forest plots.
allstudies A logical indicating whether studies with inestimable treatment effects should
be included in the forest plot.
weight.study A character string indicating weighting used to determine size of squares or dia-
monds (argument type.study) to plot individual study results. One of missing,
"same", "fixed", or "random", can be abbreviated. Plot symbols have the same
size for all studies or represent study weights from fixed effect or random effects
model.
forest.meta 29

weight.subgroup
A character string indicating weighting used to determine size of squares or
diamonds (argument type.subgroup) to plot subgroup results. One of missing,
"same", or "weight", can be abbreviated. Plot symbols have the same size for
all subgroup results or represent subgroup weights from fixed effect or random
effects model.
pscale A numeric giving scaling factor for printing of single event probabilities or risk
differences, i.e. if argument sm is equal to "PLOGIT", "PLN", "PRAW", "PAS",
"PFT", or "RD".
irscale A numeric defining a scaling factor for printing of single incidence rates or in-
cidence rate differences, i.e. if argument sm is equal to "IR", "IRLN", "IRS",
"IRFT", or "IRD".
irunit A character specifying the time unit used to calculate rates, e.g., person-years.
ref A numerical giving the reference value to be plotted as a line in the forest plot.
No reference line is plotted if argument ref is equal to NA.
lower.equi A numerical giving the lower limit of equivalence to be plotted as a line in the
forest plot. No line is plotted if argument lower.equi is equal to NA.
upper.equi A numerical giving the upper limit of equivalence to be plotted as a line in the
forest plot. No line is plotted if argument upper.equi is equal to NA.
lty.equi Line type (limits of equivalence).
col.equi Line colour (limits of equivalence).
fill.equi Colour of area between limits of equivalence.
leftcols A character vector specifying (additional) columns to be printed on the left side
of the forest plot or a logical value (see Details).
rightcols A character vector specifying (additional) columns to be printed on the right
side of the forest plot or a logical value (see Details).
leftlabs A character vector specifying labels for (additional) columns on left side of the
forest plot (see Details).
rightlabs A character vector specifying labels for (additional) columns on right side of the
forest plot (see Details).
label.e Label to be used for experimental group in table heading.
label.c Label to be used for control group in table heading.
label.e.attach A character specifying the column name where label label.e should be at-
tached to in table heading.
label.c.attach A character specifying the column name where label label.c should be at-
tached to in table heading.
label.right Graph label on right side of forest plot.
label.left Graph label on left side of forest plot.
bottom.lr A logical indicating whether labels on right and left side should be printed at
bottom or top of forest plot.
lab.NA A character string to label missing values.
30 forest.meta

lab.NA.effect A character string to label missing values in individual treatment estimates and
confidence intervals.
lab.NA.weight A character string to label missing weights.
lwd The line width, see par.
at The points at which tick-marks are to be drawn, see grid.xaxis.
label A logical value indicating whether to draw the labels on the tick marks, or an
expression or character vector which specify the labels to use. See grid.xaxis.
type.study A character string or vector specifying how to plot treatment effects and confi-
dence intervals for individual studies (see Details).
type.fixed A character string specifying how to plot treatment effect and confidence interval
for fixed effect meta-analysis (see Details).
type.random A character string specifying how to plot treatment effect and confidence interval
for random effects meta-analysis (see Details).
type.subgroup A character string specifying how to plot treatment effect and confidence interval
for subgroup results (see Details).
type.subgroup.fixed
A character string specifying how to plot treatment effect and confidence interval
for subgroup results (fixed effect model).
type.subgroup.random
A character string specifying how to plot treatment effect and confidence interval
for subgroup results (random effects model).
col.study The colour for individual study results and confidence limits.
col.square The colour for squares reflecting study’s weight in the meta-analysis.
col.square.lines
The colour for the outer lines of squares reflecting study’s weight in the meta-
analysis.
col.inside The colour for individual study results and confidence limits if confidence limits
are completely within squares.
col.inside.fixed
The colour for result of fixed effect meta-analysis if confidence limit lies com-
pletely within square.
col.inside.random
The colour for result of random effects meta-analysis if confidence limit lies
completely within square.
col.diamond The colour of diamonds representing the results for fixed effect and random
effects models.
col.diamond.fixed
The colour of diamonds for fixed effect estimates.
col.diamond.random
The colour of diamonds for random effects estimates.
col.diamond.lines
The colour of the outer lines of diamonds representing the results for fixed effect
and random effects models.
forest.meta 31

col.diamond.lines.fixed
The colour of the outer lines of diamond for fixed effect estimate.
col.diamond.lines.random
The colour of the outer lines of diamond for random effects estimate.
col.predict Background colour of prediction interval.
col.predict.lines
Colour of outer lines of prediction interval.
col.by The colour to print information on subgroups.
col.label.right
The colour for label on right side of null effect.
col.label.left The colour for label on left side of null effect.
hetstat Either a logical value indicating whether to print results for heterogeneity mea-
sures at all or a character string (see Details).
overall.hetstat
A logical value indicating whether to print heterogeneity measures for overall
treatment comparisons. This argument is useful in a meta-analysis with sub-
groups if heterogeneity statistics should only be printed on subgroup level.
hetlab Label printed in front of results for heterogeneity measures.
resid.hetstat A logical value indicating whether to print measures of residual heterogeneity
in a meta-analysis with subgroups.
resid.hetlab Label printed in front of results for residual heterogeneity measures.
print.I2 A logical value indicating whether to print the value of the I-squared statistic.
print.I2.ci A logical value indicating whether to print the confidence interval of the I-
squared statistic.
print.tau2 A logical value indicating whether to print the value of the between-study vari-
ance τ 2 .
print.tau2.ci A logical value indicating whether to print the confidence interval of τ 2 .
print.tau A logical value indicating whether to print τ , the square root of the between-
study variance τ 2 .
print.tau.ci A logical value indicating whether to print the confidence interval of τ .
print.Q A logical value indicating whether to print the value of the heterogeneity statistic
Q.
print.pval.Q A logical value indicating whether to print the p-value of the heterogeneity
statistic Q.
print.Rb A logical value indicating whether to print the value of the I-squared statistic.
print.Rb.ci A logical value indicating whether to print the confidence interval of the I-
squared statistic.
text.subgroup.nohet
A logical value or character string which is printed to indicate subgroups with
less than two studies contributing to meta-analysis (and thus without hetero-
geneity). If FALSE, heterogeneity statistics are printed (with NAs).
LRT A logical value indicating whether to report Likelihood-Ratio or Wald-type test
of heterogeneity for generalized linear mixed models.
32 forest.meta

test.overall A logical value indicating whether to print results of test for overall effect.
test.overall.fixed
A logical value indicating whether to print results of test for overall effect (fixed
effect model).
test.overall.random
A logical value indicating whether to print results of test for overall effect (ran-
dom effects model).
label.test.overall.fixed
Label printed in front of results of test for overall effect (fixed effect model).
label.test.overall.random
Label printed in front of results of test for overall effect (random effects model).
print.stat A logical value indicating whether z- or t-value for test of treatment effect should
be printed.
test.subgroup A logical value indicating whether to print results of test for subgroup differ-
ences.
test.subgroup.fixed
A logical value indicating whether to print results of test for subgroup differ-
ences (fixed effect model).
test.subgroup.random
A logical value indicating whether to print results of test for subgroup differ-
ences (random effects model).
prediction.subgroup
A single logical or logical vector indicating whether / which prediction intervals
should be printed for subgroups.
print.Q.subgroup
A logical value indicating whether to print the value of the heterogeneity statistic
Q (test for subgroup differences).
label.test.subgroup.fixed
Label printed in front of results of test for subgroup differences (fixed effect
model).
label.test.subgroup.random
Label printed in front of results of test for subgroup differences (random effects
model).
test.effect.subgroup
A single logical or logical vector indicating whether / which tests for effect in
subgroups should be printed.
test.effect.subgroup.fixed
A single logical or logical vector indicating whether / which tests for effect in
subgroups should be printed (fixed effect model).
test.effect.subgroup.random
A single logical or logical vector indicating whether / which tests for effect in
subgroups should be printed (random effects model).
label.test.effect.subgroup.fixed
Label printed in front of results of test for effect in subgroups (fixed effect
model).
forest.meta 33

label.test.effect.subgroup.random
Label printed in front of results of test for effect in subgroups (random effects
model).
text.addline1 Text for first additional line (below meta-analysis results).
text.addline2 Text for second additional line (below meta-analysis results).
fontsize The size of text (in points), see gpar.
fontfamily The font family, see gpar.
fs.heading The size of text for column headings, see gpar.
fs.fixed The size of text for results of fixed effect model, see gpar.
fs.random The size of text for results of random effects model, see gpar.
fs.predict The size of text for results of prediction interval, see gpar.
fs.fixed.labels
The size of text for label of fixed effect model, see gpar.
fs.random.labels
The size of text for label of random effects model, see gpar.
fs.predict.labels
The size of text for label of prediction interval, see gpar.
fs.study The size of text for results of individual studies, see gpar.
fs.study.labels
The size of text for labels of individual studies, see gpar.
fs.hetstat The size of text for heterogeneity measures, see gpar.
fs.test.overall
The size of text of test for overall effect, see gpar.
fs.test.subgroup
The size of text of test of subgroup differences, see gpar.
fs.test.effect.subgroup
The size of text of test of effect in subgroups, see gpar.
fs.addline The size of text for additional lines, see gpar.
fs.axis The size of text on x-axis, see gpar.
fs.smlab The size of text of label for summary measure, see gpar.
fs.xlab The size of text of label on x-axis, see gpar.
fs.lr The size of text of label on left and right side of forest plot, see gpar.
ff.heading The fontface for column headings, see gpar.
ff.fixed The fontface of text for results of fixed effect model, see gpar.
ff.random The fontface of text for results of random effects model, see gpar.
ff.predict The fontface of text for results of prediction interval, see gpar.
ff.fixed.labels
The fontface of text for label of fixed effect model, see gpar.
ff.random.labels
The fontface of text for label of random effects model, see gpar.
34 forest.meta

ff.predict.labels
The fontface of text for label of prediction interval, see gpar.
ff.study The fontface of text for results of individual studies, see gpar.
ff.study.labels
The fontface of text for labels of individual studies, see gpar.
ff.hetstat The fontface of text for heterogeneity measures, see gpar.
ff.test.overall
The fontface of text of test for overall effect, see gpar.
ff.test.subgroup
The fontface of text for test of subgroup differences, see gpar.
ff.test.effect.subgroup
The fontface of text for test of effect in subgroups, see gpar.
ff.addline The fontface of text for additional lines, see gpar.
ff.axis The fontface of text on x-axis, see gpar.
ff.smlab The fontface of text of label for summary measure, see gpar.
ff.xlab The fontface of text of label on x-axis, see gpar.
ff.lr The fontface of text of label on left and right side of forest plot, see gpar.
squaresize A numeric used to increase or decrease the size of squares in the forest plot.
plotwidth Either a character string, e.g., "8cm", "60mm", or "3inch", or a unit object
specifying width of the forest plot.
colgap Either a character string or a unit object specifying gap between columns printed
on left and right side of forest plot.
colgap.left Either a character string or a unit object specifying gap between columns printed
on left side of forest plot.
colgap.right Either a character string or a unit object specifying gap between columns printed
on right side of forest plot.
colgap.studlab Either a character string or a unit object specifying gap between column with
study labels and subsequent column.
colgap.forest Either a character string or a unit object specifying gap between column adja-
cent to forest plot and the forest plot.
colgap.forest.left
Either a character string or a unit object specifying gap between column on the
left side of forest plot and the forest plot.
colgap.forest.right
Either a character string or a unit object specifying gap between column on the
right side of forest plot and the forest plot.
calcwidth.pooled
A logical indicating whether text for fixed effect and random effects model
should be considered to calculate width of the column with study labels.
calcwidth.fixed
A logical indicating whether text given in arguments text.fixed and text.fixed.w
should be considered to calculate width of the column with study labels.
forest.meta 35

calcwidth.random
A logical indicating whether text given in arguments text.random and text.random.w
should be considered to calculate width of the column with study labels.
calcwidth.predict
A logical indicating whether text given in argument text.predict and text.predict.w
should be considered to calculate width of the column with study labels.
calcwidth.hetstat
A logical indicating whether text for heterogeneity statistics should be consid-
ered to calculate width of the column with study labels.
calcwidth.tests
A logical indicating whether text for tests of overall effect or subgroup differ-
ences should be considered to calculate width of the column with study labels.
calcwidth.subgroup
A logical indicating whether text with subgroup labels should be considered to
calculate width of the column with study labels.
calcwidth.addline
A logical indicating whether text for additional lines should be considered to
calculate width of the column with study labels.
just Justification of text in all columns but columns with study labels and additional
variables (possible values: "left", "right", "center").
just.studlab Justification of text for study labels (possible values: "left", "right", "center").
just.addcols Justification of text for additional columns (possible values: "left", "right", "cen-
ter").
just.addcols.left
Justification of text for additional columns on left side of forest plot (possible
values: "left", "right", "center"). Can be of same length as number of additional
columns on left side of forest plot.
just.addcols.right
Justification of text for additional columns on right side of forest plot (possible
values: "left", "right", "center"). Can be of same length as number of additional
columns on right side of forest plot.
spacing A numeric determining line spacing in a forest plot.
addrow A logical value indicating whether an empty row is printed above and below
study results.
addrow.overall A logical value indicating whether an empty row is printed above overall meta-
analysis results.
addrow.subgroups
A logical value indicating whether an empty row is printed between results for
subgroups.
addrows.below.overall
A numeric value indicating how many empty rows are printed between meta-
analysis results and heterogeneity statistics and test results.
new A logical value indicating whether a new figure should be printed in an existing
graphics window.
36 forest.meta

backtransf A logical indicating whether results should be back transformed in forest plots.
If backtransf = TRUE, results for sm = "OR" are presented as odds ratios rather
than log odds ratios and results for sm = "ZCOR" are presented as correlations
rather than Fisher’s z transformed correlations, for example.
digits Minimal number of significant digits for treatment effects, see print.default.
digits.se Minimal number of significant digits for standard errors, see print.default.
digits.stat Minimal number of significant digits for z- or t-statistic for test of overall effect,
see print.default.
digits.pval Minimal number of significant digits for p-value of overall treatment effect, see
print.default.
digits.pval.Q Minimal number of significant digits for p-value of heterogeneity test, see print.default.
digits.Q Minimal number of significant digits for heterogeneity statistic Q, see print.default.
digits.tau2 Minimal number of significant digits for between-study variance, see print.default.
digits.tau Minimal number of significant digits for square root of between-study variance,
see print.default.
digits.I2 Minimal number of significant digits for I-squared statistic, see print.default.
digits.weight Minimal number of significant digits for weights, see print.default.
digits.mean Minimal number of significant digits for means; only applies to metacont ob-
jects.
digits.sd Minimal number of significant digits for standard deviations; only applies to
metacont objects.
digits.cor Minimal number of significant digits for correlations; only applies to metacor
objects.
digits.time Minimal number of significant digits for times; only applies to metainc and
metarate objects.
digits.addcols A vector or scalar with minimal number of significant digits for additional columns.
digits.addcols.right
A vector or scalar with minimal number of significant digits for additional columns
on right side of forest plot.
digits.addcols.left
A vector or scalar with minimal number of significant digits for additional columns
on left side of forest plot.
scientific.pval
A logical specifying whether p-values should be printed in scientific notation,
e.g., 1.2345e-01 instead of 0.12345.
big.mark A character used as thousands separator.
zero.pval A logical specifying whether p-values should be printed with a leading zero.
JAMA.pval A logical specifying whether p-values for test of overall effect should be printed
according to JAMA reporting standards.
... Additional graphical arguments.
forest.meta 37

Details
A forest plot, also called confidence interval plot, is drawn in the active graphics window. The forest
functions in R package meta are based on the grid graphics system. In order to print the forest plot,
resize the graphics window and either use dev.copy2eps or dev.copy2pdf. Another possibility
is to create a file using pdf, png, or svg and to specify the width and height of the graphic (see
Examples).

Default layout for studies and pooled effects:

By default, treatment estimates and confidence intervals are plotted in the following way:
• For an individual study, a square with treatment estimate in the center and confidence interval
as line extending either side of the square (type.study = "square")
• For meta-analysis results, a diamond with treatment estimate in the center and right and
left side corresponding to lower and upper confidence limits (type.fixed = "diamond",
type.random = "diamond", and type.subgroup = "diamond")
In a forest plot, size of the squares typically reflects the precision of individual treatment esti-
mates based either on the fixed effect (weight.study = "fixed") or random effects meta-analysis
(weight.study = "random"). Information from meta-analysis object x is utilised if argument
weight.study is missing. Weights from the fixed effect model are used if argument x$fixed is
TRUE; weights from the random effects model are used if argument x$random is TRUE and x$fixed
is FALSE. The same square sizes are used if weight.study = "same".
A prediction interval for treatment effect of a new study (Higgins et al., 2009) is given in the forest
plot if arguments prediction and random are TRUE. For graphical presentation of prediction
intervals the approach by Guddat et al. (2012) is used.

Columns printed on left side of forest plot:

Argument leftcols can be used to specify columns which are printed on the left side of the forest
plot. By default, i.e. if argument leftcols is NULL and layout = "meta", and depending on the
class of the meta-analysis object (which is defined by the R function used to generate the object)
a different set of columns is printed on the left side of the forest plot:

Function Value of argument leftcols

metabin c("studlab", "event.e", "n.e", "event.c", "n.c")
metacont c("studlab", "n.e", "mean.e", "sd.e", "n.c", "mean.c", "sd.c")
metacor c("studlab", "n")
metagen c("studlab", "TE", "seTE")
metainc c("studlab", "event.e", "time.e", "event.c", "time.c")
metamean c("studlab", "n", "mean", "sd")
metaprop c("studlab", "event", "n")
metarate c("studlab", "event", "time", "n")
metacum "studlab"
metainf "studlab"

Note, "studlab" must be provided for study labels in argument leftcols or rightcols in-
stead of the variable name used in the meta-analysis command. If, for example, "id" is provided
in argument leftcols as this variable was used to define study labels in the meta-analysis func-
tion, this variable will be treated as an additional variable, not as study labels.
38 forest.meta

Overlapping information on left side of forest plot:

Depending on the number of columns printed on the left side of the forest plot, information on
heterogeneity measures or statistical tests (see below) can be overlapping with the x-axis. Ar-
gument addrows.below.overall can be used to specify the number of empty rows that are
printed between meta-analysis results and information on heterogeneity measures and statisti-
cal tests. By default, no additional rows are added to the forest plot. If addrows.below.overall
= NULL, the function tries to add a sufficient number of empty rows to prevent overlapping text.
Another possibility is to manually increase the space between the columns on the left side (ar-
gument colgap.left) or between the columns on the left side and the forest plot (argument
colgap.forest.left).

Columns printed on right side of forest plot:

Argument rightcols can be used to specify columns which are printed on the right side of the
forest plot. If argument rightcols is FALSE, no columns will be printed on the right side. By
default, i.e. if argument rightcols is NULL and layout = "meta", the following columns will be
printed on the right side of the forest plot:

Meta-analysis results Value of argument rightcols

No summary c("effect", "ci")
Only fixed effect model c("effect", "ci", "w.fixed")
Only random effects model c("effect", "ci", "w.random")
Both models c("effect", "ci", "w.fixed", "w.random")

By default, estimated treatment effect and corresponding confidence interval will be printed. De-
pending on arguments fixed and random, weights of the fixed effect and/or random effects model
will be given too. For an object of class metacum or metainf only the estimated treatment effect
with confidence interval are plotted.

Column names:
The arguments leftlabs and rightlabs can be used to specify column headings which are
printed on left or right side of the forest plot. For certain columns predefined labels exist which
are used by default, i.e., if arguments leftlabs and rightlabs are NULL:

Column: studlab TE seTE n.e n.c n

Label: "Study" "TE" "seTE" "Total" "Total" "Total"

Column: event.e event.c event mean.e mean.c

Label: "Events" "Events" "Events" "Mean" "Mean"

Column: sd.e sd.c time.e time.c effect

Label: "SD" "SD" "Time" "Time" x$sm

Column: ci effect.ci w.fixed w.random

Label: x$level"%-CI" effect+ci "W(fixed)" "W(random)"

For other columns, the column name will be used as a label if no column label is defined. It
is possible to only provide labels for new columns (see Examples). Otherwise the length of
leftlabs and rightlabs must be the same as the number of printed columns. The value NA can
forest.meta 39

be used to specify columns which should use default labels (see Examples).
In pairwise meta-analysis comparing two groups (i.e., metabin, metacont, metainc, and metagen
depending on the outcome), arguments label.e and label.c are used to label columns belonging
to the two treatment groups. By default, labels defined in the meta-analysis object are used. The
columns where treatment labels are attached can be changed using arguments label.e.attach
and label.c.attach.

Information on heterogeneity and statistical tests:

Argument hetstat can be a character string to specify where to print heterogeneity information:
• row with results for fixed effect model (hetstat = "fixed"),
• row with results for random effects model (hetstat = "random").
Otherwise, information on heterogeneity measures is printed below the meta-analysis results if ar-
gument overall.hetstat = TRUE (default). The heterogeneity measures to print can be specified
(see list of arguments following overall.hetstat).
In addition, the following arguments can be used to print results for various statistical tests:

Argument Statistical test

test.overall.fixed Test for overall effect (fixed effect model)
test.overall.random Test for overall effect (random effects model)
test.effect.subgroup.fixed Test for effect in subgroup (FE model)
test.effect.subgroup.random Test for effect in subgroup (RE model)
test.subgroup.fixed Test for subgroup differences (FE model)
test.subgroup.random Test for subgroup differences (RE model)

By default, these arguments are FALSE with exception of tests for subgroup differences which
are TRUE. R function settings.meta can be used to change this default for the entire R session.
For example, use the following command to always print results of tests for an overall effect:
settings.meta(test.overall = TRUE).

Flexible printing of subgroup results:

Argument subgroup determines whether summary results are printed for subgroups. A logical
vector of length equal to the number of subgroups can be provided to determine which subgroup
summaries are printed. By default, only subgroup results based on at least two studies are printed
which is identical to use argument subgroup = k.w > 1. The order of the logical vector corre-
sponds to the order of subgroups in list element ’bylevs’ of a meta-analysis object. Argument
subgroup = k.w >= 1 can be used to show results for all subgroups (including those with a single
study).
The following arguments can be used in a similar way:
• subgroup.hetstat (heterogeneity statistic in subgroups),
• prediction.subgroup (prediction interval in subgroups),
• test.effect.subgroup (test for effect in subgroups),
• test.effect.subgroup.fixed (test for effect in subgroups, fixed effect model),
• test.effect.subgroup.random (test for effect in subgroups, random effects model).

Additional general settings:

40 forest.meta

Arguments text.fixed, text.random, and text.predict can be used to change the label to
identify overall results (fixed effect and random effects model as well as prediction interval). By
default the following text is printed:
• "Common effect model" (argument text.fixed)
• "Random effects model" (text.random)
• "Prediction interval" (text.predict)
If confidence interval levels are different for individual studies, meta-analysis, and prediction
interval (arguments level, level.ma, level.predict in meta-analysis functions, e.g., metabin),
additional information is printed, e.g., " (99%-CI)" for a 99% confidence interval in the meta-
analysis.
Argument pscale can be used to rescale single proportions or risk differences, e.g., pscale =
1000 means that proportions are expressed as events per 1000 observations. This is useful in
situations with (very) low event probabilities.
Argument irscale can be used to rescale single rates or rate differences, e.g., irscale = 1000
means that rates are expressed as events per 1000 time units, e.g., person-years. This is useful in
situations with (very) low rates. Argument irunit can be used to specify the time unit used in
individual studies (default: "person-years"). This information is printed in summaries and forest
plots if argument irscale is not equal to 1.

Forest plots in RevMan5 layout:

If argument layout = "RevMan5" (and arguments leftcols and rightcols are NULL), the layout
for forest plots used for Cochrane reviews (which are generated with Review Manager 5, https:
//training.cochrane.org/online-learning/core-software-cochrane-reviews/revman)
is reproduced:
1. All columns are printed on the left side of the forest plot (see arguments leftcols and
rightcols)
2. Tests for overall effect and subgroup differences are printed (test.overall, test.effect.subgroup,
test.subgroup)
3. Diamonds representing meta-analysis results are printed in black (diamond.fixed, diamond.random)
4. Colour of squares depends on the meta-analysis object (col.square, col.square.lines)
5. Information on effect measure and meta-analysis method is printed above the forest plot
(smlab)
6. Label "Study or Subgroup" is printed for meta-analysis with subgroups (leftlabs)

Forest plots in JAMA layout:

If argument layout = "JAMA" (and arguments leftcols and rightcols are NULL), instructions
for authors of the Journal of the American Medical Association, see https://jamanetwork.
com/journals/jama/pages/instructions-for-authors/, are taken into account:
1. Graph labels on right and left side are printed in bold font at top of forest plot (see arguments
bottom.lr and ff.lr)
2. Information on effect measure and level of confidence interval is printed at bottom of forest
plot (xlab)
3. Tests for overall effect are printed (test.overall)
4. Diamonds representing meta-analysis results are printed in lightblue (diamond.fixed, diamond.random)
5. Squares representing individual study results are printed in darkblue (col.square, col.square.lines)
forest.meta 41

6. Between-study variance τ 2 is not printed

7. Empty rows are omitted (addrow)
8. Label "Source" is printed instead of "Study" (leftlabs)
9. P-values are printed without leading zeros (zero.pval)
10. P-values are rounded to three digits (for 0.001 < p ≤ 0.01) or two digits (p > 0.01) (JAMA.pval)
Study labels according to JAMA guidelines can be generated using labels.meta.

Forest plots showing results of subgroups:

The following changes are conducted if argument layout = "subgroup" (and arguments leftcols
and rightcols are NULL) and a subgroup analysis was conducted:
1. Individual study results are omitted (see argument study.results)
2. Total number of observations is not printed (pooled.totals)
3. Label "Subgroup" is printed instead of "Study" (leftlabs)

Author(s)
Guido Schwarzer <[email protected]>

References
Guddat C, Grouven U, Bender R, Skipka G (2012): A note on the graphical presentation of predic-
tion intervals in random-effects meta-analyses. Systematic Reviews, 1, 34
Higgins JPT, Thompson SG, Spiegelhalter DJ (2009): A re-evaluation of random-effects meta-
analysis. Journal of the Royal Statistical Society: Series A, 172, 137-59

See Also
metabin, metacont, metagen, forest.metabind, settings.meta, labels.meta

Examples
data(Olkin1995)
m1 <- metabin(ev.exp, n.exp, ev.cont, n.cont,
data = Olkin1995, subset = c(41, 47, 51, 59),
sm = "RR", method = "I",
studlab = paste(author, year))

## Not run:
# Do standard (symmetric) forest plot
#
forest(m1)

## End(Not run)

# Layout of forest plot similar to Review Manager 5

#
# Furthermore, add labels on both sides of forest plot and
# prediction interval
42 forest.meta

#
forest(m1, layout = "RevMan5", fixed = FALSE,
label.right = "Favours control", col.label.right = "red",
label.left = "Favours experimental", col.label.left = "green",
prediction = TRUE)

## Not run:
# Create a PDF file forest-m1.pdf with the forest plot
#
pdf("forest-m1.pdf", width = 10, height = 3)
forest(m1)
dev.off()

# Conduct subgroup meta-analysis

#
m2 <- update(m1,
subgroup = ifelse(year < 1987, "Before 1987", "1987 and later"),
print.subgroup.name = FALSE)

# Show summary results for subgroups with at least two studies

#
forest(m2, sortvar = -TE, random = FALSE)

# Show results for all subgroups

#
forest(m2, sortvar = -TE, random = FALSE, subgroup = k.w >= 1)

# Forest plot specifying argument xlim

#
forest(m1, xlim = c(0.01, 10))

# Print results of test for overall effect

#
forest(m1, test.overall.fixed = TRUE, test.overall.random = TRUE)

# Forest plot with 'classic' layout used in R package meta,

# version < 1.6-0
#
forest(m1, col.square = "black", hetstat = FALSE)

# Change set of columns printed on left side of forest plot

# (resulting in overlapping text)
#
forest(m1, random = FALSE, leftcols = "studlab")

# Use argument 'calcwidth.hetstat' to consider text for heterogeneity

# measures in width of column with study labels
#
forest(m1, random = FALSE, leftcols = "studlab",
calcwidth.hetstat = TRUE)

# Use argument 'addrows.below.overall' to manually add two empty

forest.meta 43

# rows
#
forest(m1, random = FALSE, leftcols = "studlab", addrows = 2)

# Do not print columns on right side of forest plot

#
forest(m1, rightcols = FALSE)

# Change study label to "Author"

#
forest(m1, random = FALSE, leftlabs = c("Author", NA, NA, NA, NA))

# Just give effect estimate and 95% confidence interval on right

# side of forest plot (in one column)
#
forest(m1, rightcols = c("effect.ci"))

# Just give effect estimate and 95% confidence interval on right

# side of forest plot
#
forest(m1, rightcols = c("effect", "ci"))

# 1. Change order of columns on left side

# 2. Attach labels to columns 'event.e' and 'event.c' instead of
# columns 'n.e' and 'n.c'
#
forest(m1,
leftcols = c("studlab", "n.e", "event.e", "n.c", "event.c"),
label.e.attach = "event.e", label.c.attach = "event.c")

# Specify column labels only for variables 'year' and 'author'

# (and define digits for additional variables)
#
forest(m1,
leftcols = c("studlab", "event.e", "n.e", "event.c", "n.c", "author", "year"),
leftlabs = c("Author", "Year of Publ"))

# Center text in all columns

#
forest(m1,
leftcols = c("studlab", "event.e", "n.e", "event.c", "n.c",
"author", "year"),
leftlabs = c("Author", "Year of Publ"), hetstat = FALSE,
just = "center", just.addcols = "center", just.studlab = "center")

# Same result
#
forest(m1,
leftcols = c("studlab", "event.e", "n.e", "event.c", "n.c",
"author", "year"),
leftlabs = c("Author", "Year of Publ"), hetstat = FALSE,
just = "c", just.addcols = "c", just.studlab = "c")
44 forest.meta

# Change some fontsizes and fontfaces

#
forest(m1,
fs.study = 10, ff.study = "italic",
fs.study.label = 11, ff.study.label = "bold",
fs.axis = 5, ff.axis = "italic",
ff.smlab = "bold.italic",
ff.fixed = "plain", ff.hetstat = "plain")

# Change some colours

#
forest(m1,
col.diamond = "green", col.diamond.lines = "red",
col.study = c("green", "blue", "red", "orange"),
col.square = "pink", col.square.lines = "black")

# Sort by weight in fixed effect model

#
forest(m1, sortvar = 1 / w.fixed, random = FALSE)

# Sort by decreasing weight in fixed effect model

#
forest(m1, sortvar = -1 / w.fixed, random = FALSE)

# Sort by size of treatment effect

#
forest(m1, sortvar = TE, random = FALSE)

# Sort by size of treatment effect

#
forest(m1, sortvar = -TE, random = FALSE)

# Sort by decreasing year of publication

#
forest(m1, sortvar = -year, random = FALSE)

# Print results of test for subgroup differences (random effects

# model)
#
forest(m2, sortvar = -TE, fixed = FALSE)

# Print only subgroup results

#
forest(m2, layout = "subgroup", addrows = NULL)

# Print only subgroup results (and consider text for tests of

# subgroup differences in width of subgroup column)
#
forest(m2, layout = "subgroup", calcwidth.tests = TRUE)

# Print only subgroup results (and consider text for heterogeneity

# in width of subgroup column)
#
forest.metabind 45

forest(m2, layout = "subgroup", calcwidth.hetstat = TRUE)

## End(Not run)

forest.metabind Forest plot to display the result of a meta-analysis

Description

Draws a forest plot in the active graphics window (using grid graphics system).

Usage

## S3 method for class 'metabind'

forest(
x,
leftcols,
leftlabs,
rightcols = c("effect", "ci"),
rightlabs,
overall = FALSE,
subgroup = FALSE,
hetstat = FALSE,
overall.hetstat = FALSE,
lab.NA = "",
digits = gs("digits.forest"),
digits.se = gs("digits.se"),
digits.stat = gs("digits.stat"),
digits.pval = max(gs("digits.pval") - 2, 2),
digits.pval.Q = max(gs("digits.pval.Q") - 2, 2),
digits.Q = gs("digits.Q"),
digits.tau2 = gs("digits.tau2"),
digits.tau = gs("digits.tau"),
digits.I2 = max(gs("digits.I2") - 1, 0),
scientific.pval = gs("scientific.pval"),
big.mark = gs("big.mark"),
print.subgroup.labels = if (any(x$.meta$is.subgroup)) TRUE else FALSE,
addrow.subgroups = print.subgroup.labels,
smlab,
calcwidth.pooled = overall,
warn.deprecated = gs("warn.deprecated"),
...
)
46 forest.metabind

Arguments
x An object of class metabind.
leftcols A character vector specifying (additional) columns to be plotted on the left side
of the forest plot or a logical value (see Details).
leftlabs A character vector specifying labels for (additional) columns on left side of the
forest plot (see Details).
rightcols A character vector specifying (additional) columns to be plotted on the right side
of the forest plot or a logical value (see Details).
rightlabs A character vector specifying labels for (additional) columns on right side of the
forest plot (see Details).
overall A logical indicating whether overall summaries should be plotted. This argu-
ment is useful in a meta-analysis with subgroups if summaries should only be
plotted on group level.
subgroup A logical indicating whether subgroup results should be shown in forest plot.
This argument is useful in a meta-analysis with subgroups if summaries should
not be plotted on group level.
hetstat Either a logical value indicating whether to print results for heterogeneity mea-
sures at all or a character string (see Details).
overall.hetstat
A logical value indicating whether to print heterogeneity measures for overall
treatment comparisons. This argument is useful in a meta-analysis with sub-
groups if heterogeneity statistics should only be printed on subgroup level.
lab.NA A character string to label missing values.
digits Minimal number of significant digits for treatment effects, see print.default.
digits.se Minimal number of significant digits for standard errors, see print.default.
digits.stat Minimal number of significant digits for z- or t-statistic for test of overall effect,
see print.default.
digits.pval Minimal number of significant digits for p-value of overall treatment effect, see
print.default.
digits.pval.Q Minimal number of significant digits for p-value of heterogeneity test, see print.default.
digits.Q Minimal number of significant digits for heterogeneity statistic Q, see print.default.
digits.tau2 Minimal number of significant digits for between-study variance, see print.default.
digits.tau Minimal number of significant digits for square root of between-study variance,
see print.default.
digits.I2 Minimal number of significant digits for I-squared statistic, see print.default.
scientific.pval
A logical specifying whether p-values should be printed in scientific notation,
e.g., 1.2345e-01 instead of 0.12345.
big.mark A character used as thousands separator.
print.subgroup.labels
A logical indicating whether subgroup label should be printed.
forest.metabind 47

addrow.subgroups
A logical value indicating whether an empty row is printed between results for
subgroups.
smlab A label for the summary measurex (printed at top of figure).
calcwidth.pooled
A logical indicating whether text for fixed effect and random effects model
should be considered to calculate width of the column with study labels.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
... Additional graphical arguments (passed on to forest.meta).

Details

A forest plot, also called confidence interval plot, is drawn in the active graphics window. The forest
functions in R package meta are based on the grid graphics system. In order to print the forest plot,
resize the graphics window and either use dev.copy2eps or dev.copy2pdf. Another possibility
is to create a file using pdf, png, or svg and to specify the width and height of the graphic (see
forest.meta examples).
The arguments leftcols and rightcols can be used to specify columns which are plotted on the
left and right side of the forest plot, respectively.
The arguments leftlabs and rightlabs can be used to specify column headings which are plotted
on left and right side of the forest plot, respectively. For certain columns predefined labels exist.
For other columns, the column name will be used as a label. It is possible to only provide labels
for new columns (see forest.meta examples). Otherwise the length of leftlabs and rightlabs
must be the same as the number of printed columns, respectively. The value NA can be used to
specify columns which should use default labels.
Argument hetstat can be a character string to specify where to print heterogeneity information:

• row with results for fixed effect model (hetstat = "fixed"),

• row with results for random effects model (hetstat = "random"),
• rows with ’study’ information (hetstat = "study").

Otherwise, information on heterogeneity is printed in dedicated rows.

Author(s)

Guido Schwarzer <[email protected]>

See Also

forest.meta, metabin, metacont, metagen, metabind, settings.meta

48 funnel.meta

Examples
data(Fleiss1993cont)

# Add some (fictitious) grouping variables:

#
Fleiss1993cont$age <- c(55, 65, 55, 65, 55)
Fleiss1993cont$region <- c("Europe", "Europe", "Asia", "Asia", "Europe")

m1 <- metacont(n.psyc, mean.psyc, sd.psyc, n.cont, mean.cont, sd.cont,

data = Fleiss1993cont, sm = "MD")

# Conduct two subgroup analyses

#
mu1 <- update(m1, subgroup = age, bylab = "Age group")
mu2 <- update(m1, subgroup = region, bylab = "Region")

# Combine subgroup meta-analyses and show forest plot with subgroup

# results
#
mb1 <- metabind(mu1, mu2)
mb1
forest(mb1)

funnel.meta Funnel plot

Description
Draw a funnel plot which can be used to assess small study effects in meta-analysis. A contour-
enhanced funnel plot can also be produced to assess causes of funnel plot asymmetry.

Usage
## S3 method for class 'meta'
funnel(
x,
xlim = NULL,
ylim = NULL,
xlab = NULL,
ylab = NULL,
fixed = x$fixed,
random = x$random,
axes = TRUE,
pch = if (!inherits(x, "trimfill")) 21 else ifelse(x$trimfill, 1, 21),
text = NULL,
cex = 1,
lty.fixed = 2,
funnel.meta 49

lty.random = 9,
lwd = 1,
lwd.fixed = lwd,
lwd.random = lwd,
col = "black",
bg = "darkgray",
col.fixed = "black",
col.random = "black",
log,
yaxis,
contour.levels = NULL,
col.contour,
ref = ifelse(is.relative.effect(x$sm), 1, 0),
level = if (fixed | random) x$level else NULL,
studlab = FALSE,
cex.studlab = 0.8,
pos.studlab = 2,
ref.triangle = FALSE,
lty.ref = 1,
lwd.ref = lwd,
col.ref = "black",
lty.ref.triangle = 5,
backtransf = x$backtransf,
...
)

Arguments
x An object of class meta.
xlim The x limits (min,max) of the plot.
ylim The y limits (min,max) of the plot.
xlab A label for the x-axis.
ylab A label for the y-axis.
fixed A logical indicating whether the fixed effect / common effect estimate should be
plotted.
random A logical indicating whether the random effects estimate should be plotted.
axes A logical indicating whether axes should be drawn on the plot.
pch The plotting symbol used for individual studies.
text A character vector specifying the text to be used instead of plotting symbol.
cex The magnification to be used for plotting symbol.
lty.fixed Line type (fixed effect estimate).
lty.random Line type (random effects estimate).
lwd The line width for confidence intervals (if level is not NULL).
lwd.fixed The line width for fixed effect estimate (if fixed is not NULL).
50 funnel.meta

lwd.random The line width for random effects estimate (if random is not NULL).
col A vector with colour of plotting symbols.
bg A vector with background colour of plotting symbols (only used if pch in 21:25).
col.fixed Colour of line representing fixed effect estimate.
col.random Colour of line representing random effects estimate.
log A character string which contains "x" if the x-axis is to be logarithmic, "y" if the
y-axis is to be logarithmic and "xy" or "yx" if both axes are to be logarithmic.
yaxis A character string indicating which type of weights are to be used. Either "se",
"invvar", "invse", code"size", code"invsqrtsize", or code"ess".
contour.levels A numeric vector specifying contour levels to produce contour-enhanced funnel
plot.
col.contour Colour of contours.
ref Reference value (null effect) used to produce contour-enhanced funnel plot.
level The confidence level utilised in the plot. For the funnel plot, confidence limits
are not drawn if yaxis="size" or yaxis="invsqrtsize".
studlab A logical indicating whether study labels should be printed in the graph. A
vector with study labels can also be provided (must be of same length as x$TE
then).
cex.studlab Size of study labels, see argument cex in text.
pos.studlab Position of study labels, see argument pos in text.
ref.triangle A logical indicating whether approximate confidence limits should be printed
around reference value (null effect).
lty.ref Line type (reference value).
lwd.ref The line width for the reference value and corresponding confidence intervals
(if ref.triangle is TRUE and level is not NULL).
col.ref Colour of line representing reference value.
lty.ref.triangle
Line type (confidence intervals of reference value).
backtransf A logical indicating whether results for relative summary measures (argument
sm equal to "OR", "RR", "HR", or "IRR") should be back transformed in funnel
plots. If backtransf=TRUE, results for sm="OR" are printed as odds ratios rather
than log odds ratios, for example.
... Additional graphical arguments (ignored at the moment).

Details
A funnel plot (Light & Pillemer, 1984) is drawn in the active graphics window. If fixed is TRUE,
the estimate of the fixed effect model is plotted as a vertical line. Similarly, if random is TRUE,
the estimate of the random effects model is plotted. If level is not NULL, the corresponding
approximate confidence limits are drawn around the fixed effect estimate (if fixed is TRUE) or the
random effects estimate (if random is TRUE and fixed is FALSE).
In the funnel plot, the standard error of the treatment estimates is plotted on the y-axis by de-
fault (yaxis = "se") which is likely to be the best choice (Sterne & Egger, 2001). Only exception
funnel.meta 51

is meta-analysis of diagnostic test accuracy studies (Deeks et al., 2005) where the inverse of the
square root of the effective study size is used (yaxis = "ess"). Other possible choices for yaxis are
"invvar" (inverse of the variance), "invse" (inverse of the standard error), "size" (study size),
and "invsqrtsize" (1 / sqrt(study size)).
If argument yaxis is not equal to "size", "invsqrtsize" or "ess", contour-enhanced funnel plots
can be produced (Peters et al., 2008) by specifying the contour levels (argument contour.levels).
By default (argument col.contour missing), suitable gray levels will be used to distinguish the
contours. Different colours can be chosen by argument col.contour.

Author(s)
Guido Schwarzer <[email protected]>, Petra Graham <[email protected]>

References
Deeks JJ, Macaskill P, Irwig L (2005): The performance of tests of publication bias and other
sample size effects in systematic reviews of diagnostic test accuracy was assessed. Journal of
Clinical Epidemiology, 58:882–93
Light RJ & Pillemer DB (1984): Summing Up. The Science of Reviewing Research. Cambridge:
Harvard University Press
Peters JL, Sutton AJ, Jones DR, Abrams KR, Rushton L (2008): Contour-enhanced meta-analysis
funnel plots help distinguish publication bias from other causes of asymmetry. Journal of Clinical
Epidemiology, 61, 991–6
Sterne JAC & Egger M (2001): Funnel plots for detecting bias in meta-analysis: Guidelines on
choice of axis. Journal of Clinical Epidemiology, 54, 1046–55

See Also
metabias, metabin, metagen, radial

Examples
data(Olkin1995)
m1 <- metabin(ev.exp, n.exp, ev.cont, n.cont,
data = Olkin1995, subset = c(41, 47, 51, 59),
studlab = paste(author, year),
sm = "RR", method = "I")

oldpar <- par(mfrow = c(2, 2))

# Standard funnel plot

#
funnel(m1)

# Funnel plot with confidence intervals, fixed effect estimate and

# contours
#
cc <- funnel(m1, fixed = TRUE,
level = 0.95, contour = c(0.9, 0.95, 0.99))$col.contour
legend(0.05, 0.05,
52 gs

c("0.1 > p > 0.05", "0.05 > p > 0.01", "< 0.01"), fill = cc)

# Contour-enhanced funnel plot with user-chosen colours

#
funnel(m1, fixed = TRUE,
level = 0.95, contour = c(0.9, 0.95, 0.99),
col.contour = c("darkgreen", "green", "lightgreen"),
lwd = 2, cex = 2, pch = 16, studlab = TRUE, cex.studlab = 1.25)
legend(0.05, 0.05,
c("0.1 > p > 0.05", "0.05 > p > 0.01", "< 0.01"),
fill = c("darkgreen", "green", "lightgreen"))

par(oldpar)

gs Get default for a meta-analysis setting.

Description

Get default for a meta-analysis setting in R package meta.

Usage

gs(x)

Arguments

x A character string holding a settings name.

Details

This function can be used to get the default for a meta-analysis setting defined using settings.meta.
This function is primarily used to define default settings in meta-analysis functions, e.g., metabin or
metacont. A list of all arguments with current settings is printed using the command settings.meta("print").

Author(s)

Guido Schwarzer <[email protected]>

See Also

settings.meta
JAMAlabels 53

Examples
# Get default setting for Hartung-Knapp method
#
gs("hakn")

# Get default setting for summary measure in metabin()

#
gs("smbin")

JAMAlabels Create study labels in JAMA layout (deprecated function)

Description

Deprecated function to create study labels in JAMA layout (for forest plot). Replaced by labels.meta.

Usage

JAMAlabels(author, year, citation, data = NULL)

Arguments

author A vector providing study authors.

year A vector providing year of publication.
citation A vector providing citation numbers.
data An optional data frame containing the study information.

Details

This auxiliary function can be used to create study labels in JAMA layout which can be added to a
forest plot using argument ’studlab’.

Author(s)

Guido Schwarzer <[email protected]>

See Also

labels.meta, forest.meta
54 labbe.metabin

Examples
data(Fleiss1993bin)

refs <- 20 + 1:7

Fleiss1993bin$mylabs <-
JAMAlabels(study, year, refs, data = Fleiss1993bin)

m <- metabin(d.asp, n.asp, d.plac, n.plac, data = Fleiss1993bin,

studlab = paste(study, year),
sm = "OR", random = FALSE)

forest(m, studlab = mylabs, layout = "JAMA",

fontfamily = "Times", fontsize = 10)

labbe.metabin L’Abbé plot for meta-analysis with binary outcomes

Description
Draw a L’Abbé plot for meta-analysis with binary outcomes.

Usage
## S3 method for class 'metabin'
labbe(
x,
xlim,
ylim,
xlab = NULL,
ylab = NULL,
TE.fixed = x$TE.fixed,
TE.random = x$TE.random,
fixed = x$fixed,
random = x$random,
backtransf = x$backtransf,
axes = TRUE,
pch = 21,
text = NULL,
cex = 1,
col = "black",
bg = "lightgray",
lwd = 1,
lwd.fixed = lwd,
lwd.random = lwd,
lty.fixed = 2,
lty.random = 9,
labbe.metabin 55

col.fixed = col,
col.random = col,
nulleffect = TRUE,
lwd.nulleffect = lwd,
col.nulleffect = "lightgray",
sm = x$sm,
weight,
studlab = FALSE,
cex.studlab = 0.8,
pos.studlab = 2,
label.e = x$label.e,
label.c = x$label.c,
...
)

## Default S3 method:
labbe(
x,
y,
xlim,
ylim,
xlab = NULL,
ylab = NULL,
TE.fixed = NULL,
TE.random = NULL,
fixed = !is.null(TE.fixed),
random = !is.null(TE.random),
backtransf = TRUE,
axes = TRUE,
pch = 21,
text = NULL,
cex = 1,
col = "black",
bg = "lightgray",
lwd = 1,
lwd.fixed = lwd,
lwd.random = lwd,
lty.fixed = 2,
lty.random = 9,
col.fixed = col,
col.random = col,
nulleffect = TRUE,
lwd.nulleffect = lwd,
col.nulleffect = "lightgray",
sm = "",
weight,
studlab = FALSE,
cex.studlab = 0.8,
56 labbe.metabin

pos.studlab = 2,
label.e = NULL,
label.c = NULL,
...
)

Arguments
x An object of class metabin. Alternatively, the x coordinates of points of the
L’Abbé plot.
xlim The x limits (min, max) of the plot.
ylim The y limits (min, max) of the plot.
xlab A label for the x-axis.
ylab A label for the y-axis.
TE.fixed A numeric or vector specifying combined fixed effect estimate(s).
TE.random A numeric or vector specifying combined random effects estimate(s).
fixed A logical indicating whether the fixed effect estimate should be plotted.
random A logical indicating whether the random effects estimate should be plotted.
backtransf A logical indicating which values should be printed on x- and y-axis (see De-
tails).
axes A logical indicating whether axes should be drawn on the plot.
pch The plotting symbol used for individual studies.
text A character vector specifying the text to be used instead of plotting symbol.
cex The magnification to be used for plotting symbol.
col A vector with colour of plotting symbols.
bg A vector with background colour of plotting symbols (only used if pch in 21:25).
lwd The line width.
lwd.fixed The line width(s) for fixed effect estimate(s) (if fixed is not NULL or FALSE).
lwd.random The line width(s) for random effects estimate(s) (if random is not NULL or FALSE).
lty.fixed Line type(s) for fixed effect estimate(s).
lty.random Line type(s) for random effects estimate(s).
col.fixed Colour of line(s) for fixed effect estimate(s).
col.random Colour of line(s) for random effects estimate(s).
nulleffect A logical indicating whether line for null effect should be added to the plot..
lwd.nulleffect Width of line for null effect.
col.nulleffect Colour of line for null effect.
sm A character string indicating underlying summary measure, i.e., "RD", "RR",
"OR", or "ASD".
labbe.metabin 57

weight Either a numeric vector specifying relative sizes of plotting symbols or a char-
acter string indicating which type of plotting symbols is to be used for indi-
vidual treatment estimates. One of missing (see Details), "same", "fixed", or
"random", can be abbreviated. Plot symbols have the same size for all studies
or represent study weights from fixed effect or random effects model.
studlab A logical indicating whether study labels should be printed in the graph. A vec-
tor with study labels can also be provided (must be of same length as x$event.e
then).
cex.studlab Size of study labels.
pos.studlab Position of study labels, see argument pos in text.
label.e Label for experimental group.
label.c Label for control group.
... Graphical arguments as in par may also be passed as arguments.
y The y coordinates of the L’Abbé plot, if argument x is not an object of class
metabin.

Details
A L’Abbé plot is a scatter plot with the risk in the control group on the x-axis and the risk in the
experimental group on the y-axis (L’Abbé et al., 1987). It can be used to evaluate heterogeneity in
meta-analysis. Furthermore, this plot can aid to choose a summary measure (odds ratio, risk ratio,
risk difference) that will result in more consistent results (Jiménez et al., 1997; Deeks, 2002).
If argument backtransf is TRUE (default), event probabilities will be printed on x- and y-axis.
Otherwise, transformed event probabilities will be printed as defined by the summary measure, i.e.,
log odds of probabilities for odds ratio as summary measure (sm = "OR"), log probabilities for sm =
"RR", and arcsine-transformed probabilities for sm = "ASD".
If fixed is TRUE, the estimate of the fixed effect / common effct model is plotted as a line. If
random is TRUE, the estimate of the random effects model is plotted as a line.
Information from object x is utilised if argument weight is missing. Weights from the fixed effect
model are used (weight = "fixed") if argument x$fixed is TRUE; weights from the random effects
model are used (weight = "random") if argument x$random is TRUE and x$fixed is FALSE.

Author(s)
Guido Schwarzer <[email protected]>

References
Deeks JJ (2002): Issues in the selection of a summary statistic for meta-analysis of clinical trials
with binary outcomes. Statistics in Medicine, 21, 1575–600
Jiménez FJ, Guallar E, Martín-Moreno JM (1997): A graphical display useful for meta-analysis.
European Journal of Public Health, 1, 101–5
L’Abbé KA, Detsky AS, O’Rourke K (1987): Meta-analysis in clinical research. Annals of Internal
Medicine, 107, 224–33
58 labels.meta

# L'Abbe plot for risk ratio

#
labbe(m1)

# L'Abbe plot for odds ratio

#
labbe(m1, sm = "OR")
# same plot
labbe(update(m1, sm = "OR"))

# L'Abbe plot for risk difference

#
labbe(m1, sm = "RD")

# L'Abbe plot on log odds scale

#
labbe(m1, sm = "OR", backtransf = FALSE)

# L'Abbe plot for odds ratio with coloured lines for various
# treatment effects (defined as log odds ratios)
#
mycols <- c("blue", "yellow", "green", "red", "green", "yellow", "blue")
labbe(m1, sm = "OR", random = FALSE,
TE.fixed = log(c(1 / 10, 1 / 5, 1 / 2, 1, 2, 5, 10)),
col.fixed = mycols, lwd.fixed = 2)

# L'Abbe plot on log odds scale with coloured lines for various
# treatment effects (defined as log odds ratios)
#
labbe(m1, sm = "OR", random = FALSE, backtransf = FALSE,
TE.fixed = log(c(1 / 10, 1 / 5, 1 / 2, 1, 2, 5, 10)),
col.fixed = mycols, lwd.fixed = 2)

labels.meta Create study labels for forest plot

Description
Create study labels for forest plot.
labels.meta 59

Usage
## S3 method for class 'meta'
labels(
object,
author = object$studlab,
year = "",
citation = NULL,
layout = "JAMA",
data = object$data,
...
)

Arguments
object An object of class meta.
author An optional vector providing study authors.
year An optional vector providing year of publication.
citation An optional vector providing citation numbers.
layout A character string specifying layout. Either "JAMA" or "Lancet".
data An optional data frame containing the study information.
... Additional arguments (ignored at the moment).

Details
This auxiliary function can be used to create study labels in JAMA or Lancet layout which can be
added to a forest plot using argument ’studlab’.

Author(s)
Guido Schwarzer <[email protected]>

refs <- 20 + 1:7

m <- metabin(d.asp, n.asp, d.plac, n.plac, data = Fleiss1993bin,

studlab = study, sm = "OR", random = FALSE)

forest(m,
studlab = labels(m, year = year, citation = refs, layout = "JAMA"),
layout = "JAMA", fontfamily = "Times", fontsize = 10)
60 longarm

forest(m,
studlab = labels(m, year = year, citation = refs, layout = "Lancet"))

longarm Transform data from pairwise comparisons to long arm-based format

Description
This function transforms data from pairwise comparisons to a long arm-based format, i.e., two rows
for a pairwise comparison.

Usage
longarm(
treat1,
treat2,
event1,
n1,
event2,
n2,
mean1,
sd1,
mean2,
sd2,
time1,
time2,
data = NULL,
studlab,
append = TRUE,
keep.duplicated = FALSE,
keep.internal = FALSE
)

Arguments
treat1 Either label for first treatment or a meta-analysis or pairwise object (see Details).
treat2 Label for second treatment.
event1 Number of events (first treatment).
n1 Number of observations (first treatment).
event2 Number of events (second treatment).
n2 Number of observations (second treatment)
mean1 Estimated mean (first treatment).
sd1 Standard deviation (first treatment).
mean2 Estimated mean (second treatment).
longarm 61

sd2 Standard deviation (second treatment).

time1 Person time at risk (first treatment)
time2 Person time at risk (second treatment)
data An optional data frame containing the study information.
studlab A vector with study labels (optional).
append A logical indicating if data frame provided in argument ’data’ should be re-
turned.
keep.duplicated
A logical indicating if duplicated rows should be returned (see Details).
keep.internal A logical indicating if variables generated internally should be returned (typi-
cally only relevant for data checking).

Details
This function transforms data given as one pairwise comparison per row to a long arm-based format
with one row per treatment arm. The long arm-based format is, for example, the required input
format for WinBUGS.
The function can be used to transform data with a binary, continuous or count outcome. The cor-
responding meta-analysis functions are metabin, metacont and metainc. Accordingly, a meta-
analysis object created with one of these functions can be provided as argument treat1. It is also
possible to use the longarm function with an R objected created with pairwise from R package
netmeta.
Otherwise, arguments treat1 and treat2 are mandatory to identify the individual treatments and,
depending on the outcome, the following additional arguments are mandatory:

• event1, n1, event2, n2 (binary outcome);

• n1, mean1, sd1, n2, mean2, sd2 (continuous outcome);
• time1, n1, time2, n2 (count outcome).

Argument studlab must be provided if several pairwise comparisons come from a single study
with more than two treatments.
The following variables will be returned:

studlab study label

treat treatment label
n group sample size (count outcome only if provided)
events number of events (binary or count outcome)
nonevents number of non-events (binary outcome)
mean estimated mean (continuous outcome)
sd standard deviation (continuous outcome)
time person time at risk (count outcome)

In addition, the data set provided in argument data will be returned if argument append = TRUE
(default).
62 metabias.meta

Argument keep.duplicated can be used to keep duplicated rows from the data set. Duplicated
rows can occur, for example, in a three-arm study comparing treatments A and B with placebo. In
this situation, the placebo arm will be returned twice in the data set in long arm-based format if
keep.duplicated = TRUE. By default, duplicated rows with not be kept in the data set.

Value
A data frame in long arm-based format.

Note
R function to.long from R package metafor is called internally.

Author(s)
Guido Schwarzer <[email protected]>

See Also
metabin, metacont, metainc, pairwise

Examples
# Artificial example with three studies
m <- metabin(1:3, 100:102, 4:6, 200:202, studlab = LETTERS[1:3])
# Transform data to long arm-based format
longarm(m)
# Keep internal variables
longarm(m, keep.internal = TRUE)

metabias.meta Test for funnel plot asymmetry

Description
Test for funnel plot asymmetry, based on rank correlation or linear regression method.

Usage
## S3 method for class 'meta'
metabias(
x,
method.bias = x$method.bias,
plotit = FALSE,
correct = FALSE,
k.min = 10,
...
)
metabias.meta 63

## S3 method for class 'metabias'

print(
x,
digits = gs("digits"),
digits.stat = gs("digits.stat"),
digits.pval = max(gs("digits.pval"), 2),
digits.se = gs("digits.se"),
digits.tau2 = gs("digits.tau2"),
scientific.pval = gs("scientific.pval"),
big.mark = gs("big.mark"),
zero.pval = gs("zero.pval"),
JAMA.pval = gs("JAMA.pval"),
text.tau2 = gs("text.tau2"),
...
)

metabias(x, ...)

## Default S3 method:
metabias(
x,
seTE,
method.bias = "Egger",
plotit = FALSE,
correct = FALSE,
k.min = 10,
...
)

Arguments
x An object of class meta or estimated treatment effect in individual studies.
method.bias A character string indicating which test is to be used (see Details), can be abbre-
viated.
plotit A logical indicating whether a plot should be produced (see Details).
correct A logical indicating whether a continuity corrected statistic is used for rank cor-
relation tests.
k.min Minimum number of studies to perform test for funnel plot asymmetry.
... Additional arguments passed on to rma.uni.
digits Minimal number of significant digits for estimates, see print.default.
digits.stat Minimal number of significant digits for z- or t-value of test for test of funnel
plot asymmetry, see print.default.
digits.pval Minimal number of significant digits for p-value of test for test of funnel plot
asymmetry, see print.default.
digits.se Minimal number of significant digits for standard errors, see print.default.
64 metabias.meta

digits.tau2 Minimal number of significant digits for residual heterogeneity variance, see
print.default.
scientific.pval
A logical specifying whether p-values should be printed in scientific notation,
e.g., 1.2345e-01 instead of 0.12345.
big.mark A character used as thousands separator.
zero.pval A logical specifying whether p-values should be printed with a leading zero.
JAMA.pval A logical specifying whether p-values for test of overall effect should be printed
according to JAMA reporting standards.
text.tau2 Text printed to identify residual heterogeneity variance τ 2 .
seTE Standard error of estimated treatment effect (mandatory if x not of class meta).

Details
Functions to conduct rank correlation or linear regression tests for funnel plot asymmetry.

Classic generic tests: The following tests are generic tests for funnel plot asymmetry which only
require estimates of the treatment effect and corresponding standard errors. Accordingly, these
are the only tests provided by R function metabias.default.
If argument method.bias is "Begg", the test statistic is based on the rank correlation between
standardised treatment estimates and variance estimates of estimated treatment effects; Kendall’s
tau is used as correlation measure (Begg & Mazumdar, 1994). The test statistic follows a stan-
dard normal distribution. By default (if correct is FALSE), no continuity correction is utilised
(Kendall & Gibbons, 1990).
If argument method.bias is "Egger", the test statistic is based on a weighted linear regression
of the treatment effect on its standard error (Egger et al., 1997). The test statistic follows a t
distribution with number of studies -2 degrees of freedom.
If argument method.bias is "Thompson", the test statistic is based on a weighted linear regression
of the treatment effect on its standard error using an additive between-study variance component
denoted as methods (3a) - (3d) in Thompson & Sharp (1999). The test statistic follows a t distri-
bution with number of studies -2 degrees of freedom.

Tests for meta-analysis with binary outcomes: The following tests for funnel plot asymmetry
are only available for meta-analyses comparing two binary outcomes, i.e. meta-analyses generated
with the metabin function. The only exception is the test by Peters et al. (2006) which can also
be used in a meta-analysis of single proportions generated with metaprop.
If argument method.bias is "Harbord", the test statistic is based on a weighted linear regression
utilising efficient score and score variance (Harbord et al., 2006, 2009). The test statistic follows
a t distribution with number of studies -2 degrees of freedom.
In order to calculate an arcsine test for funnel plot asymmetry (Rücker et al., 2008), one has to
use the metabin function with argument sm = "ASD" as input to the metabias command. The
three arcsine tests described in Rücker et al. (2008) can be calculated by setting method.bias to
"Begg", "Egger" and "Thompson", respectively.
If argument method.bias is "Macaskill", the test statistic is based on a weighted linear regres-
sion of the treatment effect on the total sample size with weights reciprocal to the variance of
the average event probability (Macaskill et al., 2001, method FPV). The test statistic follows a t
distribution with number of studies -2 degrees of freedom.
metabias.meta 65

If argument method.bias is "Peters", the test statistic is based on a weighted linear regression of
the treatment effect on the inverse of the total sample size with weights reciprocal to the variance
of the average event probability (Peters et al., 2006). The test statistic follows a t distribution with
number of studies -2 degrees of freedom. Note, this test is a variant of Macaskill et al. (2001),
method FPV, using the inverse sample size as covariate.
If argument method.bias is "Schwarzer", the test statistic is based on the rank correlation be-
tween a standardised cell frequency and the inverse of the variance of the cell frequency; Kendall’s
tau is used as correlation measure (Schwarzer et al., 2007). The test statistic follows a stan-
dard normal distribution. By default (if correct is FALSE), no continuity correction is utilised
(Kendall & Gibbons, 1990).
Finally, for meta-analysis of diagnostic test accuracy studies, if argument method.bias is "Deeks",
the test statistic is based on a weighted linear regression of the log diagnostic odds ratio on the in-
verse of the squared effective sample size using the effective sample size as weights (Deeks et al.,
2005). The test statistic follows a t distribution with number of studies -2 degrees of freedom.

Test for the standardised mean difference: If argument method.bias is "Pustejovsky",

the test statistic is based on a weighted linear regression of the treatment effect on the square
root of the sum of the inverse group sample sizes using the treatment effect variance as weights
(Pustejovsky & Rodgers, 2019). The test statistic follows a t distribution with number of studies
-2 degrees of freedom.

Recommendations and default settings: Following recommendations by Sterne et al. (2011),

by default, a test for funnel plot asymmetry is only conducted if the number of studies is ten
or larger (argument k.min = 10). This behaviour can be changed by setting a smaller value for
argument k.min. Note, the minimum number of studies is three.
If argument method.bias is missing, the Harbord test (method.bias = "Harbord") is used in
meta-analysis of binary outcomes for the odds ratio as effect measure and the Egger test (method.bias
= "Egger") in all other settings (Sterne et al., 2011).
No test for funnel plot asymmetry is conducted in meta-analyses with subgroups.

If argument plotit = TRUE, a scatter plot is shown if argument method.bias is equal to "Begg",
"Egger", "Thompson", "Harbord", or "Deeks".

Value
A list with class metabias containing the following components if a test for funnel plot asymmetry
is conducted:
statistic Test statistic.
df The degrees of freedom of the test statistic in the case that it follows a t distri-
bution.
pval The p-value for the test.
estimate Estimates used to calculate test statisic.
method A character string indicating what type of test was used.
title Title of Cochrane review.
complab Comparison label.
outclab Outcome label.
66 metabias.meta

var.model A character string indicating whether none, multiplicative, or additive residual

heterogeneity variance was assumed.
method.bias As defined above.
x Meta-analysis object.
version Version of R package meta used to create object.

Or a list with the following elements if test is not conducted due to the number of studies:

k Number of studies in meta-analysis.

k.min Minimum number of studies to perform test for funnel plot asymmetry.
version Version of R package meta used to create object.

Author(s)
Guido Schwarzer <[email protected]>

References
Begg CB & Mazumdar M (1994): Operating characteristics of a rank correlation test for publication
bias. Biometrics, 50, 1088–101
Deeks JJ, Macaskill P, Irwig L (2005): The performance of tests of publication bias and other
sample size effects in systematic reviews of diagnostic test accuracy was assessed. Journal of
Clinical Epidemiology, 58:882–93
Egger M, Smith GD, Schneider M & Minder C (1997): Bias in meta-analysis detected by a simple,
graphical test. British Medical Journal, 315, 629–34
Harbord RM, Egger M & Sterne J (2006): A modified test for small-study effects in meta-analyses
of controlled trials with binary endpoints. Statistics in Medicine, 25, 3443–57
Harbord RM, Harris RJ, Sterne JAC (2009): Updated tests for small-study effects in meta–analyses.
The Stata Journal, 9, 197–210
Kendall M & Gibbons JD (1990): Rank Correlation Methods. London: Edward Arnold
Macaskill P, Walter SD, Irwig L (2001): A comparison of methods to detect publication bias in
meta-analysis. Statistics in Medicine, 20, 641–54
Peters JL, Sutton AJ, Jones DR, Abrams KR & Rushton L (2006): Comparison of two methods to
detect publication bias in meta-analysis. Journal of the American Medical Association, 295, 676–80
Pustejovsky JE, Rodgers MA (2019): Testing for funnel plot asymmetry of standardized mean
differences. Research Synthesis Methods, 10, 57–71
Rücker G, Schwarzer G, Carpenter JR (2008): Arcsine test for publication bias in meta-analyses
with binary outcomes. Statistics in Medicine, 27, 746–63
Schwarzer G, Antes G & Schumacher M (2007): A test for publication bias in meta-analysis with
sparse binary data. Statistics in Medicine, 26, 721–33
Sterne, JAC et al. (2011): Recommendations for examining and interpreting funnel plot asymmetry
in meta-analyses of randomised controlled trials. BMJ (Clinical research ed.), 343, 1
Thompson SG & Sharp, SJ (1999): Explaining heterogeneity in meta-analysis: a comparison of
methods, Statistics in Medicine, 18, 2693–708
metabias.rm5 67

See Also
funnel, funnel.meta, metabin, metacont, metagen

Examples
data(Olkin1995)
m1 <- metabin(ev.exp, n.exp, ev.cont, n.cont,
data = Olkin1995, subset = 1:10, sm = "RR", method = "I")

metabias(m1)
metabias(m1, plotit = TRUE)

metabias(m1, method.bias = "Begg")

metabias(m1, method.bias = "Begg", correct = TRUE)

metabias(m1, method.bias = "Schwarzer")

metabias(m1, method.bias = "Egger")$pval

# Arcsine test (based on linear regression)

#
m1.as <- update(m1, sm = "ASD")
metabias(m1.as)
# Same result (using function metabias.default)
metabias(m1.as$TE, m1.as$seTE)

# No test for funnel plot asymmetry calculated

#
m2 <- update(m1, subset = 1:5)
metabias(m2)

m3 <- update(m1, subset = 1:2)

metabias(m3)

# Test for funnel plot asymmetry calculated (use of argument k.min)

#
metabias(m2, k.min = 5)

metabias.rm5 Cochrane review: Test for funnel plot asymmetry

Description
Conduct a test for funnel plot asymmetry for all outcomes in a Cochrane review

Usage
## S3 method for class 'rm5'
metabias(
68 metabias.rm5

x,
comp.no,
outcome.no,
method.bias = "linreg",
method.bias.binary = method.bias,
method.bias.or = "score",
k.min = 10,
...
)

Arguments
x An object of class rm5.
comp.no Comparison number.
outcome.no Outcome number.
method.bias A character string indicating which test for small-study effects is to be used
for all outcomes. Either "rank", "linreg", or "mm", can be abbreviated. See
function metabias
method.bias.binary
A character string indicating which test is to be used for binary outcomes. Either
"rank", "linreg", "mm", "count", "score", or "peters", can be abbreviated.
See function metabias
method.bias.or A character string indicating which test is to be used for binary outcomes with
odds ratio as summary measure. Either "rank", "linreg", "mm", "count",
"score", or "peters", can be abbreviated. See function metabias
k.min Minimum number of studies to perform test for small-study effects.
... Additional arguments (ignored at the moment)

Details
This function can be used to conduct a test for funnel plot asymmetry for all or selected meta-
analyses in a Cochrane Review.
Review Manager 5 (RevMan 5) is the current software used for preparing and maintaining Cochrane
Reviews (https://training.cochrane.org/online-learning/core-software-cochrane-reviews/
revman). In RevMan 5, subgroup analyses can be defined and data from a Cochrane review can be
imported to R using the function read.rm5.
The R function metacr is called internally.

Author(s)
Guido Schwarzer <[email protected]>

References
Higgins, J.P.T and S. Green (2011): Cochrane Handbook for Systematic Reviews of Interventions
Version 5.1.0 [Updated March 2011]. The Cochrane Library: http://www.cochrane-handbook.org/
metabin 69

See Also
metabias, metacr, read.rm5, summary.rm5

Examples
# Locate export data file "Fleiss1993_CR.csv" in sub-directory of
# package "meta"
#
filename <- system.file("extdata", "Fleiss1993_CR.csv", package = "meta")
Fleiss1993_CR <- read.rm5(filename)

# Print results for all tests of small-study effects

#
metabias(Fleiss1993_CR, k.min = 5)

# Print result of test of small-study effects for second outcome in

# first comparison
#
metabias(Fleiss1993_CR, comp.no = 1, outcome.no = 2, k.min = 5)

metabin Meta-analysis of binary outcome data

Description
Calculation of fixed effect and random effects estimates (risk ratio, odds ratio, risk difference, arc-
sine difference, or diagnostic odds ratio) for meta-analyses with binary outcome data. Mantel-
Haenszel, inverse variance, Peto method, generalised linear mixed model (GLMM), and sample size
method are available for pooling. For GLMMs, the rma.glmm function from R package metafor
(Viechtbauer, 2010) is called internally.

Usage
metabin(
event.e,
n.e,
event.c,
n.c,
studlab,
data = NULL,
subset = NULL,
exclude = NULL,
method = ifelse(tau.common, "Inverse", gs("method")),
sm = ifelse(!is.na(charmatch(tolower(method), c("peto", "glmm", "ssw"), nomatch =
NA)), "OR", gs("smbin")),
incr = gs("incr"),
allincr = gs("allincr"),
70 metabin

addincr = gs("addincr"),
allstudies = gs("allstudies"),
MH.exact = gs("MH.exact"),
RR.Cochrane = gs("RR.Cochrane"),
Q.Cochrane = gs("Q.Cochrane") & method == "MH" & method.tau == "DL",
model.glmm = gs("model.glmm"),
level = gs("level"),
level.ma = gs("level.ma"),
fixed = gs("fixed"),
random = gs("random") | !is.null(tau.preset),
overall = fixed | random,
overall.hetstat = fixed | random,
hakn = gs("hakn"),
adhoc.hakn = gs("adhoc.hakn"),
method.tau = ifelse(!is.na(charmatch(tolower(method), "glmm", nomatch = NA)), "ML",
gs("method.tau")),
method.tau.ci = gs("method.tau.ci"),
tau.preset = NULL,
TE.tau = NULL,
tau.common = gs("tau.common"),
prediction = gs("prediction"),
level.predict = gs("level.predict"),
method.bias = ifelse(sm == "OR", "Harbord", ifelse(sm == "DOR", "Deeks",
gs("method.bias"))),
backtransf = gs("backtransf"),
pscale = 1,
text.fixed = gs("text.fixed"),
text.random = gs("text.random"),
text.predict = gs("text.predict"),
text.w.fixed = gs("text.w.fixed"),
text.w.random = gs("text.w.random"),
title = gs("title"),
complab = gs("complab"),
outclab = "",
label.e = gs("label.e"),
label.c = gs("label.c"),
label.left = gs("label.left"),
label.right = gs("label.right"),
subgroup,
subgroup.name = NULL,
print.subgroup.name = gs("print.subgroup.name"),
sep.subgroup = gs("sep.subgroup"),
test.subgroup = gs("test.subgroup"),
prediction.subgroup = gs("prediction.subgroup"),
byvar,
print.CMH = gs("print.CMH"),
keepdata = gs("keepdata"),
warn = gs("warn"),
metabin 71

warn.deprecated = gs("warn.deprecated"),
control = NULL,
...
)

Arguments
event.e Number of events in experimental group or true positives in diagnostic study.
n.e Number of observations in experimental group or number of ill participants in
diagnostic study.
event.c Number of events in control group or false positives in diagnostic study.
n.c Number of observations in control group or number of healthy participants in
diagnostic study.
studlab An optional vector with study labels.
data An optional data frame containing the study information, i.e., event.e, n.e, event.c,
and n.c.
subset An optional vector specifying a subset of studies to be used.
exclude An optional vector specifying studies to exclude from meta-analysis, however,
to include in printouts and forest plots.
method A character string indicating which method is to be used for pooling of studies.
One of "Inverse", "MH", "Peto", "GLMM", or "SSW", can be abbreviated.
sm A character string indicating which summary measure ("RR", "OR", "RD", "ASD",
or "DOR") is to be used for pooling of studies, see Details.
incr Could be either a numerical value which is added to each cell frequency for
studies with a zero cell count or the character string "TACC" which stands for
treatment arm continuity correction, see Details.
allincr A logical indicating if incr is added to each cell frequency of all studies if at
least one study has a zero cell count. If FALSE (default), incr is added only to
each cell frequency of studies with a zero cell count.
addincr A logical indicating if incr is added to each cell frequency of all studies irre-
spective of zero cell counts.
allstudies A logical indicating if studies with zero or all events in both groups are to be in-
cluded in the meta-analysis (applies only if sm is equal to "RR", "OR", or "DOR").
MH.exact A logical indicating if incr is not to be added to all cell frequencies for studies
with a zero cell count to calculate the pooled estimate based on the Mantel-
Haenszel method.
RR.Cochrane A logical indicating if 2*incr instead of 1*incr is to be added to n.e and n.c
in the calculation of the risk ratio (i.e., sm="RR") for studies with a zero cell.
This is used in RevMan 5, the program for preparing and maintaining Cochrane
reviews.
Q.Cochrane A logical indicating if the Mantel-Haenszel estimate is used in the calculation of
the heterogeneity statistic Q which is implemented in RevMan 5, the program
for preparing and maintaining Cochrane reviews.
72 metabin

model.glmm A character string indicating which GLMM should be used. One of "UM.FS",
"UM.RS", "CM.EL", and "CM.AL", see Details.
level The level used to calculate confidence intervals for individual studies.
level.ma The level used to calculate confidence intervals for meta-analysis estimates.
fixed A logical indicating whether a fixed effect / common effect meta-analysis should
be conducted.
random A logical indicating whether a random effects meta-analysis should be con-
ducted.
overall A logical indicating whether overall summaries should be reported. This argu-
ment is useful in a meta-analysis with subgroups if overall results should not be
reported.
overall.hetstat
A logical value indicating whether to print heterogeneity measures for overall
treatment comparisons. This argument is useful in a meta-analysis with sub-
groups if heterogeneity statistics should only be printed on subgroup level.
hakn A logical indicating whether the method by Hartung and Knapp should be used
to adjust test statistics and confidence intervals.
adhoc.hakn A character string indicating whether an ad hoc variance correction should be
applied in the case of an arbitrarily small Hartung-Knapp variance estimate, see
Details.
method.tau A character string indicating which method is used to estimate the between-
study variance τ 2 and its square root τ . Either "DL", "PM", "REML", "ML", "HS",
"SJ", "HE", or "EB", can be abbreviated.
method.tau.ci A character string indicating which method is used to estimate the confidence
interval of τ 2 and τ . Either "QP", "BJ", or "J", or "", can be abbreviated.
tau.preset Prespecified value for the square root of the between-study variance τ 2 .
TE.tau Overall treatment effect used to estimate the between-study variance τ 2 .
tau.common A logical indicating whether tau-squared should be the same across subgroups.
prediction A logical indicating whether a prediction interval should be printed.
level.predict The level used to calculate prediction interval for a new study.
method.bias A character string indicating which test for funnel plot asymmetry is to be used.
Either "Begg", "Egger", "Thompson", "Schwarzer", "Harbord", "Peters", or
"Deeks", can be abbreviated. See function metabias.
backtransf A logical indicating whether results for odds ratio (sm="OR"), risk ratio (sm="RR"),
or diagnostic odds ratio (sm="DOR") should be back transformed in printouts and
plots. If TRUE (default), results will be presented as odds ratios and risk ratios;
otherwise log odds ratios and log risk ratios will be shown.
pscale A numeric defining a scaling factor for printing of risk differences.
text.fixed A character string used in printouts and forest plot to label the pooled fixed effect
estimate.
text.random A character string used in printouts and forest plot to label the pooled random
effects estimate.
metabin 73

text.predict A character string used in printouts and forest plot to label the prediction inter-
val.
text.w.fixed A character string used to label weights of fixed effect model.
text.w.random A character string used to label weights of random effects model.
title Title of meta-analysis / systematic review.
complab Comparison label.
outclab Outcome label.
label.e Label for experimental group.
label.c Label for control group.
label.left Graph label on left side of forest plot.
label.right Graph label on right side of forest plot.
subgroup An optional vector to conduct a meta-analysis with subgroups.
subgroup.name A character string with a name for the subgroup variable.
print.subgroup.name
A logical indicating whether the name of the subgroup variable should be printed
in front of the group labels.
sep.subgroup A character string defining the separator between name of subgroup variable and
subgroup label.
test.subgroup A logical value indicating whether to print results of test for subgroup differ-
ences.
prediction.subgroup
A logical indicating whether prediction intervals should be printed for sub-
groups.
byvar Deprecated argument (replaced by ’subgroup’).
print.CMH A logical indicating whether result of the Cochran-Mantel-Haenszel test for
overall effect should be printed.
keepdata A logical indicating whether original data (set) should be kept in meta object.
warn A logical indicating whether warnings should be printed (e.g., if incr is added
to studies with zero cell frequencies).
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
control An optional list to control the iterative process to estimate the between-study
variance τ 2 . This argument is passed on to rma.uni or rma.glmm, respectively.
... Additional arguments passed on to rma.glmm function.

Details
Calculation of fixed and random effects estimates for meta-analyses with binary outcome data.
The following measures of treatment effect are available (Rücker et al., 2009):

• Risk ratio (sm = "RR")

74 metabin

• Odds ratio (sm = "OR")

• Risk difference (sm = "RD")
• Arcsine difference (sm = "ASD")
• Diagnostic Odds ratio (sm = "DOR")

Note, mathematically, odds ratios and diagnostic odds ratios are identical, however, the labels in
printouts and figures differ.
Default settings are utilised for several arguments (assignments using gs function). These defaults
can be changed for the current R session using the settings.meta function.
Furthermore, R function update.meta can be used to rerun a meta-analysis with different settings.

Meta-analysis method:
By default, both fixed effect (also called common effect) and random effects models are consid-
ered (see arguments fixed and random). If method is "MH" (default), the Mantel-Haenszel method
(Greenland & Robins, 1985; Robins et al., 1986) is used to calculate the fixed effect estimate; if
method is "Inverse", inverse variance weighting is used for pooling (Fleiss, 1993); if method is
"Peto", the Peto method is used for pooling (Yussuf et al., 1985); if method is "SSW", the sample
size method is used for pooling (Bakbergenuly et al., 2020).
While the Mantel-Haenszel and Peto method are defined under the fixed effect model, random
effects variants based on these methods are also implemented in metabin. Following RevMan
5, the Mantel-Haenszel estimator is used in the calculation of the between-study heterogeneity
statistic Q which is used in the DerSimonian-Laird estimator. Accordlingly, the results for the
random effects meta-analysis using the Mantel-Haenszel or inverse variance method are typically
very similar. For the Peto method, Peto’s log odds ratio, i.e. (O-E) / V and its standard error
sqrt(1 / V) with O-E and V denoting "Observed minus Expected" and its variance, are utilised in
the random effects model. Accordingly, results of a random effects model using sm = "Peto" can
be different to results from a random effects model using sm = "MH" or sm = "Inverse".
A distinctive and frequently overlooked advantage of binary endpoints is that individual patient
data (IPD) can be extracted from a two-by-two table. Accordingly, statistical methods for IPD,
i.e., logistic regression and generalised linear mixed models, can be utilised in a meta-analysis
of binary outcomes (Stijnen et al., 2010; Simmonds et al., 2016). These methods are available
(argument method = "GLMM") for the odds ratio as summary measure by calling the rma.glmm
function from R package metafor internally.
Four different GLMMs are available for meta-analysis with binary outcomes using argument
model.glmm (which corresponds to argument model in the rma.glmm function):

1. Logistic regression model with fixed study effects (default)

(model.glmm = "UM.FS", i.e., Unconditional Model - Fixed Study effects)
2. Mixed-effects logistic regression model with random study effects
(model.glmm = "UM.RS", i.e., Unconditional Model - Random Study effects)
3. Generalised linear mixed model (conditional Hypergeometric-Normal)
(model.glmm = "CM.EL", i.e., Conditional Model - Exact Likelihood)
4. Generalised linear mixed model (conditional Binomial-Normal)
(model.glmm = "CM.AL", i.e., Conditional Model - Approximate Likelihood)

Details on these four GLMMs as well as additional arguments which can be provided using ar-
gument ’...’ in metabin are described in rma.glmm where you can also find information on
metabin 75

the iterative algorithms used for estimation. Note, regardless of which value is used for argu-
ment model.glmm, results for two different GLMMs are calculated: fixed effect model (with fixed
treatment effect) and random effects model (with random treatment effects).

Continuity correction:
For studies with a zero cell count, by default, 0.5 is added to all cell frequencies of these studies;
if incr is "TACC" a treatment arm continuity correction is used instead (Sweeting et al., 2004;
Diamond et al., 2007). For odds ratio and risk ratio, treatment estimates and standard errors are
only calculated for studies with zero or all events in both groups if allstudies is TRUE. This
continuity correction is used both to calculate individual study results with confidence limits and
to conduct meta-analysis based on the inverse variance method. For Peto method and GLMMs
no continuity correction is used. For the Mantel-Haenszel method, by default (if MH.exact is
FALSE), incr is added to all cell frequencies of a study with a zero cell count in the calculation
of the pooled risk ratio or odds ratio as well as the estimation of the variance of the pooled risk
difference, risk ratio or odds ratio. This approach is also used in other software, e.g. RevMan 5
and the Stata procedure metan. According to Fleiss (in Cooper & Hedges, 1994), there is no need
to add 0.5 to a cell frequency of zero to calculate the Mantel-Haenszel estimate and he advocates
the exact method (MH.exact = TRUE). Note, estimates based on exact Mantel-Haenszel method
or GLMM are not defined if the number of events is zero in all studies either in the experimental
or control group.

Estimation of between-study variance:

The following methods to estimate the between-study variance τ 2 are available for the inverse
variance method:
• DerSimonian-Laird estimator (method.tau = "DL")
• Paule-Mandel estimator (method.tau = "PM")
• Restricted maximum-likelihood estimator (method.tau = "REML")
• Maximum-likelihood estimator (method.tau = "ML")
• Hunter-Schmidt estimator (method.tau = "HS")
• Sidik-Jonkman estimator (method.tau = "SJ")
• Hedges estimator (method.tau = "HE")
• Empirical Bayes estimator (method.tau = "EB")
See metagen for more information on these estimators. Note, the maximum-likelihood method is
utilized for GLMMs.

Confidence interval for the between-study variance:

The following methods to calculate a confidence interval for τ 2 and τ are available.

Argument Method
method.tau.ci = "J" Method by Jackson
method.tau.ci = "BJ" Method by Biggerstaff and Jackson
method.tau.ci = "QP" Q-Profile method

See metagen for more information on these methods. For GLMMs, no confidence intervals
for τ 2 and τ are calculated. Likewise, no confidence intervals for τ 2 and τ are calculated if
method.tau.ci = "".
76 metabin

Hartung-Knapp method:
Hartung and Knapp (2001a,b) proposed an alternative method for random effects meta-analysis
based on a refined variance estimator for the treatment estimate. Simulation studies (Hartung and
Knapp, 2001a,b; IntHout et al., 2014; Langan et al., 2019) show improved coverage probabilities
compared to the classic random effects method.
In rare settings with very homogeneous treatment estimates, the Hartung-Knapp variance estimate
can be arbitrarily small resulting in a very narrow confidence interval (Knapp and Hartung, 2003;
Wiksten et al., 2016). In such cases, an ad hoc variance correction has been proposed by utilising
the variance estimate from the classic random effects model with the HK method (Knapp and
Hartung, 2003; IQWiQ, 2020). An alternative approach is to use the wider confidence interval of
classic fixed or random effects meta-analysis and the HK method (Wiksten et al., 2016; Jackson
et al., 2017).
Argument adhoc.hakn can be used to choose the ad hoc method:

Argument Ad hoc method

adhoc.hakn = "" not used
adhoc.hakn = "se" use variance correction if HK standard error is smaller
than standard error from classic random effects
meta-analysis (Knapp and Hartung, 2003)
adhoc.hakn = "iqwig6" use variance correction if HK confidence interval
is narrower than CI from classic random effects model
with DerSimonian-Laird estimator (IQWiG, 2020)
adhoc.hakn = "ci" use wider confidence interval of classic random effects
and HK meta-analysis
(Hybrid method 2 in Jackson et al., 2017)

For GLMMs, a method similar to Knapp and Hartung (2003) is implemented, see description of
argument tdist in rma.glmm, and the ad hoc variance correction is not available.

Prediction interval:
A prediction interval for the proportion in a new study (Higgins et al., 2009) is calculated if
arguments prediction and random are TRUE. Note, the definition of prediction intervals varies in
the literature. This function implements equation (12) of Higgins et al., (2009) which proposed a
t distribution with K-2 degrees of freedom where K corresponds to the number of studies in the
meta-analysis.

Subgroup analysis:
Argument subgroup can be used to conduct subgroup analysis for a categorical covariate. The
metareg function can be used instead for more than one categorical covariate or continuous co-
variates.

Exclusion of studies from meta-analysis:

Arguments subset and exclude can be used to exclude studies from the meta-analysis. Studies
are removed completely from the meta-analysis using argument subset, while excluded studies
are shown in printouts and forest plots using argument exclude (see Examples in metagen).
Meta-analysis results are the same for both arguments.

Presentation of meta-analysis results:

metabin 77

Value
An object of class c("metabin","meta") with corresponding print, summary, and forest func-
tions. The object is a list containing the following components:

event.e, n.e, event.c, n.c, studlab, exclude,

As defined above.
sm, method, incr, allincr, addincr,
As defined above.
allstudies, MH.exact, RR.Cochrane, Q.Cochrane, model.glmm,
As defined above.
warn, level, level.ma, fixed, random,
As defined above.
overall, overall.hetstat,
As defined above.
hakn, adhoc.hakn, method.tau, method.tau.ci,
As defined above.
tau.preset, TE.tau, method.bias,
As defined above.
tau.common, title, complab, outclab,
As defined above.
label.e, label.c, label.left, label.right,
As defined above.
subgroup, subgroup.name,
As defined above.
print.subgroup.name, sep.subgroup, warn,
As defined above.
TE, seTE Estimated treatment effect and standard error of individual studies.
lower, upper Lower and upper confidence interval limits for individual studies.
zval, pval z-value and p-value for test of treatment effect for individual studies.
w.fixed, w.random
Weight of individual studies (in fixed and random effects model).
TE.fixed, seTE.fixed
Estimated overall treatment effect, e.g., log risk ratio or risk difference, and
standard error (fixed effect model).
lower.fixed, upper.fixed
Lower and upper confidence interval limits (fixed effect model).
statistic.fixed, pval.fixed
z-value and p-value for test of overall treatment effect (fixed effect model).
78 metabin

TE.random, seTE.random
Estimated overall treatment effect, e.g., log risk ratio or risk difference, and
standard error (random effects model).
lower.random, upper.random
Lower and upper confidence interval limits (random effects model).
statistic.random, pval.random
z-value or t-value and corresponding p-value for test of overall treatment effect
(random effects model).
prediction, level.predict
As defined above.
seTE.predict Standard error utilised for prediction interval.
lower.predict, upper.predict
Lower and upper limits of prediction interval.
k Number of studies combined in meta-analysis.
Q Heterogeneity statistic Q.
df.Q Degrees of freedom for heterogeneity statistic.
pval.Q P-value of heterogeneity test.
Q.LRT Heterogeneity statistic for likelihood-ratio test (only if method = "GLMM").
df.Q.LRT Degrees of freedom for likelihood-ratio test
pval.Q.LRT P-value of likelihood-ratio test.
tau2 Between-study variance τ 2 .
se.tau2 Standard error of τ 2 .
lower.tau2, upper.tau2
Lower and upper limit of confidence interval for τ 2 .
tau Square-root of between-study variance τ .
lower.tau, upper.tau
Lower and upper limit of confidence interval for τ .
H Heterogeneity statistic H.
lower.H, upper.H
Lower and upper confidence limit for heterogeneity statistic H.
I2 Heterogeneity statistic I2 .
lower.I2, upper.I2
Lower and upper confidence limit for heterogeneity statistic I2 .
Rb Heterogeneity statistic Rb .
lower.Rb, upper.Rb
Lower and upper confidence limit for heterogeneity statistic Rb .
Q.CMH Cochran-Mantel-Haenszel test statistic for overall effect.
df.Q.CMH Degrees of freedom for Cochran-Mantel-Haenszel test statistic.
pval.Q.CMH P-value of Cochran-Mantel-Haenszel test.
incr.e, incr.c Increment added to cells in the experimental and control group, respectively.
sparse Logical flag indicating if any study included in meta-analysis has any zero cell
frequencies.
metabin 79

doublezeros Logical flag indicating if any study has zero cell frequencies in both treatment
groups.
df.hakn Degrees of freedom for test of treatment effect for Hartung-Knapp method (only
if hakn = TRUE).
k.MH Number of studies combined in meta-analysis using Mantel-Haenszel method.
bylevs Levels of grouping variable - if subgroup is not missing.
TE.fixed.w, seTE.fixed.w
Estimated treatment effect and standard error in subgroups (fixed effect model)
- if subgroup is not missing.
lower.fixed.w, upper.fixed.w
Lower and upper confidence interval limits in subgroups (fixed effect model) -
if subgroup is not missing.
statistic.fixed.w, pval.fixed.w
z-value and p-value for test of treatment effect in subgroups (fixed effect model)
- if subgroup is not missing.
TE.random.w, seTE.random.w
Estimated treatment effect and standard error in subgroups (random effects model)
- if subgroup is not missing.
lower.random.w, upper.random.w
Lower and upper confidence interval limits in subgroups (random effects model)
- if subgroup is not missing.
statistic.random.w, pval.random.w
z-value or t-value and corresponding p-value for test of treatment effect in sub-
groups (random effects model) - if subgroup is not missing.
w.fixed.w, w.random.w
Weight of subgroups (in fixed and random effects model) - if subgroup is not
missing.
df.hakn.w Degrees of freedom for test of treatment effect for Hartung-Knapp method in
subgroups - if subgroup is not missing and hakn = TRUE.
event.e.w Number of events in experimental group in subgroups - if subgroup is not miss-
ing.
n.e.w Number of observations in experimental group in subgroups - if subgroup is not
missing.
event.c.w Number of events in control group in subgroups - if subgroup is not missing.
n.c.w Number of observations in control group in subgroups - if subgroup is not miss-
ing.
k.w Number of studies combined within subgroups - if subgroup is not missing.
k.all.w Number of all studies in subgroups - if subgroup is not missing.
Q.w.fixed Overall within subgroups heterogeneity statistic Q (based on fixed effect model)
- if subgroup is not missing.
Q.w.random Overall within subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing (only calculated if argument tau.common is
TRUE).
80 metabin

df.Q.w Degrees of freedom for test of overall within subgroups heterogeneity - if subgroup
is not missing.
pval.Q.w.fixed P-value of within subgroups heterogeneity statistic Q (based on fixed effect
model) - if subgroup is not missing.
pval.Q.w.random
P-value of within subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
Q.b.fixed Overall between subgroups heterogeneity statistic Q (based on fixed effect model)
- if subgroup is not missing.
Q.b.random Overall between subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
df.Q.b Degrees of freedom for test of overall between subgroups heterogeneity - if
subgroup is not missing.
pval.Q.b.fixed P-value of between subgroups heterogeneity statistic Q (based on fixed effect
model) - if subgroup is not missing.
pval.Q.b.random
P-value of between subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
tau.w Square-root of between-study variance within subgroups - if subgroup is not
missing.
H.w Heterogeneity statistic H within subgroups - if subgroup is not missing.
lower.H.w, upper.H.w
Lower and upper confidence limit for heterogeneity statistic H within subgroups
- if subgroup is not missing.
I2.w Heterogeneity statistic I2 within subgroups - if subgroup is not missing.
lower.I2.w, upper.I2.w
Lower and upper confidence limit for heterogeneity statistic I2 within subgroups
- if subgroup is not missing.
keepdata As defined above.
data Original data (set) used in function call (if keepdata = TRUE).
subset Information on subset of original data used in meta-analysis (if keepdata =
TRUE).
.glmm.fixed GLMM object generated by call of rma.glmm function (fixed effect model).
.glmm.random GLMM object generated by call of rma.glmm function (random effects model).
call Function call.
version Version of R package meta used to create object.
version.metafor
Version of R package metafor used for GLMMs.

Author(s)
Guido Schwarzer <[email protected]>
metabin 81

References
Bakbergenuly I, Hoaglin DC, Kulinskaya E (2020): Methods for estimating between-study variance
and overall effect in meta-analysis of odds-ratios. Research Synthesis Methods, DOI: 10.1002/jrsm.1404
Cooper H & Hedges LV (1994): The Handbook of Research Synthesis. Newbury Park, CA: Russell
Sage Foundation
Diamond GA, Bax L, Kaul S (2007): Uncertain Effects of Rosiglitazone on the Risk for Myocardial
Infarction and Cardiovascular Death. Annals of Internal Medicine, 147, 578–81
DerSimonian R & Laird N (1986): Meta-analysis in clinical trials. Controlled Clinical Trials, 7,
177–88
Fleiss JL (1993): The statistical basis of meta-analysis. Statistical Methods in Medical Research, 2,
121–45
Greenland S & Robins JM (1985): Estimation of a common effect parameter from sparse follow-up
data. Biometrics, 41, 55–68
Hartung J & Knapp G (2001): A refined method for the meta-analysis of controlled clinical trials
with binary outcome. Statistics in Medicine, 20, 3875–89
Higgins JPT, Thompson SG, Spiegelhalter DJ (2009): A re-evaluation of random-effects meta-
analysis. Journal of the Royal Statistical Society: Series A, 172, 137–59
IQWiG (2020): General Methods: Version 6.0. https://www.iqwig.de/en/about-us/methods/
methods-paper/
Knapp G & Hartung J (2003): Improved tests for a random effects meta-regression with a single
covariate. Statistics in Medicine, 22, 2693–710
Review Manager (RevMan) [Computer program]. Version 5.4. The Cochrane Collaboration, 2020
Paule RC & Mandel J (1982): Consensus values and weighting factors. Journal of Research of the
National Bureau of Standards, 87, 377–85
Pettigrew HM, Gart JJ, Thomas DG (1986): The bias and higher cumulants of the logarithm of a
binomial variate. Biometrika, 73, 425–35
Robins J, Breslow N, Greenland S (1986): Estimators of the Mantel-Haenszel Variance Consistent
in Both Sparse Data and Large-Strata Limiting Models. Biometrics, 42, 311–23
Rücker G, Schwarzer G, Carpenter J, Olkin I (2009): Why add anything to nothing? The arcsine
difference as a measure of treatment effect in meta-analysis with zero cells. Statistics in Medicine,
28, 721–38
Simmonds MC, Higgins JP (2016): A general framework for the use of logistic regression models
in meta-analysis. Statistical Methods in Medical Research, 25, 2858–77
StataCorp. 2011. Stata Statistical Software: Release 12. College Station, TX: StataCorp LP.
Stijnen T, Hamza TH, Ozdemir P (2010): Random effects meta-analysis of event outcome in the
framework of the generalized linear mixed model with applications in sparse data. Statistics in
Medicine, 29, 3046–67
Sweeting MJ, Sutton AJ, Lambert PC (2004): What to add to nothing? Use and avoidance of
continuity corrections in meta-analysis of sparse data. Statistics in Medicine, 23, 1351–75
Viechtbauer W (2010): Conducting meta-analyses in R with the metafor package. Journal of Sta-
tistical Software, 36, 1–48
82 metabin

Wiksten A, Rücker G, Schwarzer G (2016): Hartung-Knapp method is not always conservative

compared with fixed-effect meta-analysis. Statistics in Medicine, 35, 2503–15
Yusuf S, Peto R, Lewis J, Collins R, Sleight P (1985): Beta blockade during and after myocardial
infarction: An overview of the randomized trials. Progress in Cardiovascular Diseases, 27, 335–71

See Also
update.meta, forest, funnel, metabias, metacont, metagen, metareg, print.meta

Examples
# Calculate odds ratio and confidence interval for a single study
#
metabin(10, 20, 15, 20, sm = "OR")

# Different results (due to handling of studies with double zeros)

#
metabin(0, 10, 0, 10, sm = "OR")
metabin(0, 10, 0, 10, sm = "OR", allstudies = TRUE)

# Use subset of Olkin (1995) to conduct meta-analysis based on

# inverse variance method (with risk ratio as summary measure)
#
data(Olkin1995)
m1 <- metabin(ev.exp, n.exp, ev.cont, n.cont,
data = Olkin1995, subset = c(41, 47, 51, 59), method = "Inverse")
m1
# Show results for individual studies
summary(m1)

# Use different subset of Olkin (1995)

#
m2 <- metabin(ev.exp, n.exp, ev.cont, n.cont,
data = Olkin1995, subset = year < 1970, studlab = author,
method = "Inverse")
m2
forest(m2)

# Meta-analysis with odds ratio as summary measure

#
m3 <- metabin(ev.exp, n.exp, ev.cont, n.cont,
data = Olkin1995, subset = year < 1970,
sm = "OR", method = "Inverse", studlab = author)
# Same meta-analysis result using 'update.meta' function
m3 <- update(m2, sm = "OR")
m3

# Meta-analysis based on Mantel-Haenszel method (with odds ratio as

# summary measure)
#
m4 <- update(m3, method = "MH")
m4
metabin 83

# Meta-analysis based on Peto method (only available for odds ratio

# as summary measure)
#
m5 <- update(m3, method = "Peto")
m5

## Not run:
# Meta-analysis using generalised linear mixed models
# (only if R package 'lme4' is available)
#

# Logistic regression model with (k = 4) fixed study effects

# (default: model.glmm = "UM.FS")
#
m6 <- metabin(ev.exp, n.exp, ev.cont, n.cont,
data = Olkin1995, subset = year < 1970, method = "GLMM")
# Same results:
m6 <- update(m2, method = "GLMM")
m6

# Mixed-effects logistic regression model with random study effects

# (warning message printed due to argument 'nAGQ')
#
m7 <- update(m6, model.glmm = "UM.RS")
#
# Use additional argument 'nAGQ' for internal call of 'rma.glmm'
# function
#
m7 <- update(m6, model.glmm = "UM.RS", nAGQ = 1)
m7

# Generalised linear mixed model (conditional Hypergeometric-Normal)

# (R package 'BiasedUrn' must be available)
#
m8 <- update(m6, model.glmm = "CM.EL")
m8

# Generalised linear mixed model (conditional Binomial-Normal)

#
m9 <- update(m6, model.glmm = "CM.AL")
m9

# Logistic regression model with (k = 70) fixed study effects

# (about 18 seconds with Intel Core i7-3667U, 2.0GHz)
#
m10 <- metabin(ev.exp, n.exp, ev.cont, n.cont,
data = Olkin1995, method = "GLMM")
m10

# Mixed-effects logistic regression model with random study effects

# - about 50 seconds with Intel Core i7-3667U, 2.0GHz
# - several warning messages, e.g. "failure to converge, ..."
84 metabind

#
update(m10, model.glmm = "UM.RS")

# Conditional Hypergeometric-Normal GLMM

# - long computation time (about 12 minutes with Intel Core
# i7-3667U, 2.0GHz)
# - estimation problems for this very large dataset:
# * warning that Choleski factorization of Hessian failed
# * confidence interval for treatment effect smaller in random
# effects model compared to fixed effect model
#
system.time(m11 <- update(m10, model.glmm = "CM.EL"))
m11

# Generalised linear mixed model (conditional Binomial-Normal)

# (less than 1 second with Intel Core i7-3667U, 2.0GHz)
#
update(m10, model.glmm = "CM.AL")

## End(Not run)

metabind Combine and summarize meta-analysis objects

Description
This function can be used to combine meta-analysis objects and is, for example, useful to summarize
results of various meta-analysis methods or to generate a forest plot with results of several subgroup
analyses.

Usage
metabind(..., name = NULL, pooled = NULL, backtransf = NULL, outclab = NULL)

Arguments
... Any number of meta-analysis objects or a single list with meta-analyses.
name An optional character vector providing descriptive names for the meta-analysis
objects.
pooled A character string or vector indicating whether results of a fixed effect or ran-
dom effects model should be considered. Either "fixed" or "random", can be
abbreviated.
backtransf A logical indicating whether results should be back transformed in printouts and
plots. If backtransf=TRUE (default), results for sm="OR" are printed as odds
ratios rather than log odds ratios, for example.
outclab Outcome label for all meta-analyis objects.
metabind 85

Details
This function can be used to combine any number of meta-analysis objects which is useful, for
example, to summarize results of various meta-analysis methods or to generate a forest plot with
results of several subgroup analyses (see Examples).
Individual study results are not retained with metabind. This is possible using R function metamerge
which, however, can only be used to combine results of two meta-analyses.

Value
An object of class c("metabind","meta") with corresponding print, summary, and forest func-
tions. See metagen for more information on list elements.

Author(s)
Guido Schwarzer <[email protected]>

See Also
metagen, forest.metabind, metamerge

Examples
data(Fleiss1993cont)

# Add some (fictitious) grouping variables:

#
Fleiss1993cont$age <- c(55, 65, 55, 65, 55)
Fleiss1993cont$region <- c("Europe", "Europe", "Asia", "Asia", "Europe")

m1 <- metacont(n.psyc, mean.psyc, sd.psyc, n.cont, mean.cont, sd.cont,

data = Fleiss1993cont, sm = "MD")

# Conduct two subgroup analyses

#
mu1 <- update(m1, subgroup = age, subgroup.name = "Age group")
mu2 <- update(m1, subgroup = region, subgroup.name = "Region")

# Combine subgroup meta-analyses and show forest plot with subgroup

# results
#
mb1 <- metabind(mu1, mu2)
mb1
forest(mb1)

# Use various estimation methods for between-study heterogeneity

# variance
#
m1.pm <- update(m1, method.tau = "PM")
m1.dl <- update(m1, method.tau = "DL")
m1.ml <- update(m1, method.tau = "ML")
m1.hs <- update(m1, method.tau = "HS")
86 metacont

m1.sj <- update(m1, method.tau = "SJ")

m1.he <- update(m1, method.tau = "HE")
m1.eb <- update(m1, method.tau = "EB")

# Combine meta-analyses and show results

#
taus <- c("Restricted maximum-likelihood estimator",
"Paule-Mandel estimator",
"DerSimonian-Laird estimator",
"Maximum-likelihood estimator",
"Hunter-Schmidt estimator",
"Sidik-Jonkman estimator",
"Hedges estimator",
"Empirical Bayes estimator")
#
m1.taus <- metabind(m1, m1.pm, m1.dl, m1.ml, m1.hs, m1.sj, m1.he, m1.eb,
name = taus, pooled = "random")
m1.taus
forest(m1.taus, print.I2 = FALSE, print.pval.Q = FALSE)

metacont Meta-analysis of continuous outcome data

Description
Calculation of fixed and random effects estimates for meta-analyses with continuous outcome data;
inverse variance weighting is used for pooling.

Usage
metacont(
n.e,
mean.e,
sd.e,
n.c,
mean.c,
sd.c,
studlab,
data = NULL,
subset = NULL,
exclude = NULL,
id = NULL,
median.e,
q1.e,
q3.e,
min.e,
max.e,
median.c,
metacont 87

q1.c,
q3.c,
min.c,
max.c,
method.mean = "Luo",
method.sd = "Shi",
approx.mean.e,
approx.mean.c = approx.mean.e,
approx.sd.e,
approx.sd.c = approx.sd.e,
sm = gs("smcont"),
pooledvar = gs("pooledvar"),
method.smd = gs("method.smd"),
sd.glass = gs("sd.glass"),
exact.smd = gs("exact.smd"),
method.ci = gs("method.ci.cont"),
level = gs("level"),
level.ma = gs("level.ma"),
fixed = gs("fixed"),
random = gs("random") | !is.null(tau.preset),
overall = fixed | random,
overall.hetstat = fixed | random,
hakn = gs("hakn"),
adhoc.hakn = gs("adhoc.hakn"),
method.tau = gs("method.tau"),
method.tau.ci = gs("method.tau.ci"),
tau.preset = NULL,
TE.tau = NULL,
tau.common = gs("tau.common"),
prediction = gs("prediction"),
level.predict = gs("level.predict"),
method.bias = gs("method.bias"),
backtransf = gs("backtransf"),
text.fixed = gs("text.fixed"),
text.random = gs("text.random"),
text.predict = gs("text.predict"),
text.w.fixed = gs("text.w.fixed"),
text.w.random = gs("text.w.random"),
title = gs("title"),
complab = gs("complab"),
outclab = "",
label.e = gs("label.e"),
label.c = gs("label.c"),
label.left = gs("label.left"),
label.right = gs("label.right"),
subgroup,
subgroup.name = NULL,
print.subgroup.name = gs("print.subgroup.name"),
88 metacont

sep.subgroup = gs("sep.subgroup"),
test.subgroup = gs("test.subgroup"),
prediction.subgroup = gs("prediction.subgroup"),
byvar,
keepdata = gs("keepdata"),
warn = gs("warn"),
warn.deprecated = gs("warn.deprecated"),
control = NULL,
...
)

Arguments
n.e Number of observations in experimental group.
mean.e Estimated mean in experimental group.
sd.e Standard deviation in experimental group.
n.c Number of observations in control group.
mean.c Estimated mean in control group.
sd.c Standard deviation in control group.
studlab An optional vector with study labels.
data An optional data frame containing the study information.
subset An optional vector specifying a subset of studies to be used.
exclude An optional vector specifying studies to exclude from meta-analysis, however,
to include in printouts and forest plots.
id An optional vector specifying which estimates come from the same study result-
ing in the use of a three-level meta-analysis model.
median.e Median in experimental group (used to estimate the mean and standard devia-
tion).
q1.e First quartile in experimental group (used to estimate the mean and standard
deviation).
q3.e Third quartile in experimental group (used to estimate the mean and standard
deviation).
min.e Minimum in experimental group (used to estimate the mean and standard devi-
ation).
max.e Maximum in experimental group (used to estimate the mean and standard devi-
ation).
median.c Median in control group (used to estimate the mean and standard deviation).
q1.c First quartile in control group (used to estimate the mean and standard devia-
tion).
q3.c Third quartile in control group (used to estimate the mean and standard devia-
tion).
min.c Minimum in control group (used to estimate the mean and standard deviation).
max.c Maximum in control group (used to estimate the mean and standard deviation).
metacont 89

method.mean A character string indicating which method to use to approximate the mean from
the median and other statistics (see Details).
method.sd A character string indicating which method to use to approximate the standard
deviation from sample size, median, interquartile range and range (see Details).
approx.mean.e Approximation method to estimate means in experimental group (see Details).
approx.mean.c Approximation method to estimate means in control group (see Details).
approx.sd.e Approximation method to estimate standard deviations in experimental group
(see Details).
approx.sd.c Approximation method to estimate standard deviations in control group (see
Details).
sm A character string indicating which summary measure ("MD", "SMD", or "ROM")
is to be used for pooling of studies.
pooledvar A logical indicating if a pooled variance should be used for the mean difference
(sm="MD").
method.smd A character string indicating which method is used to estimate the standardised
mean difference (sm="SMD"). Either "Hedges" for Hedges’ g (default), "Cohen"
for Cohen’s d, or "Glass" for Glass’ delta, can be abbreviated.
sd.glass A character string indicating which standard deviation is used in the denom-
inator for Glass’ method to estimate the standardised mean difference. Ei-
ther "control" using the standard deviation in the control group (sd.c) or
"experimental" using the standard deviation in the experimental group (sd.e),
can be abbreviated.
exact.smd A logical indicating whether exact formulae should be used in estimation of the
standardised mean difference and its standard error (see Details).
method.ci A character string indicating which method is used to calculate confidence in-
tervals for individual studies, see Details.
level The level used to calculate confidence intervals for individual studies.
level.ma The level used to calculate confidence intervals for meta-analysis estimates.
fixed A logical indicating whether a fixed effect / common effect meta-analysis should
be conducted.
random A logical indicating whether a random effects meta-analysis should be con-
ducted.
overall A logical indicating whether overall summaries should be reported. This argu-
ment is useful in a meta-analysis with subgroups if overall results should not be
reported.
overall.hetstat
A logical value indicating whether to print heterogeneity measures for overall
treatment comparisons. This argument is useful in a meta-analysis with sub-
groups if heterogeneity statistics should only be printed on subgroup level.
hakn A logical indicating whether the method by Hartung and Knapp should be used
to adjust test statistics and confidence intervals.
adhoc.hakn A character string indicating whether an ad hoc variance correction should be
applied in the case of an arbitrarily small Hartung-Knapp variance estimate, see
Details.
90 metacont

method.tau A character string indicating which method is used to estimate the between-
study variance τ 2 and its square root τ . Either "DL", "PM", "REML", "ML", "HS",
"SJ", "HE", or "EB", can be abbreviated.
method.tau.ci A character string indicating which method is used to estimate the confidence
interval of τ 2 and τ . Either "QP", "BJ", or "J", or "", can be abbreviated.
tau.preset Prespecified value for the square root of the between-study variance τ 2 .
TE.tau Overall treatment effect used to estimate the between-study variance tau-squared.
tau.common A logical indicating whether tau-squared should be the same across subgroups.
prediction A logical indicating whether a prediction interval should be printed.
level.predict The level used to calculate prediction interval for a new study.
method.bias A character string indicating which test is to be used. Either "Begg", "Egger",
"Thompson", or "Pustejovsky", can be abbreviated. See function metabias.
backtransf A logical indicating whether results for ratio of means (sm="ROM") should be
back transformed in printouts and plots. If TRUE (default), results will be pre-
sented as ratio of means; otherwise log ratio of means will be shown.
text.fixed A character string used in printouts and forest plot to label the pooled fixed effect
estimate.
text.random A character string used in printouts and forest plot to label the pooled random
effects estimate.
text.predict A character string used in printouts and forest plot to label the prediction inter-
val.
text.w.fixed A character string used to label weights of fixed effect model.
text.w.random A character string used to label weights of random effects model.
title Title of meta-analysis / systematic review.
complab Comparison label.
outclab Outcome label.
label.e Label for experimental group.
label.c Label for control group.
label.left Graph label on left side of forest plot.
label.right Graph label on right side of forest plot.
subgroup An optional vector to conduct a meta-analysis with subgroups.
subgroup.name A character string with a name for the subgroup variable.
print.subgroup.name
A logical indicating whether the name of the subgroup variable should be printed
in front of the group labels.
sep.subgroup A character string defining the separator between name of subgroup variable and
subgroup label.
test.subgroup A logical value indicating whether to print results of test for subgroup differ-
ences.
prediction.subgroup
A logical indicating whether prediction intervals should be printed for sub-
groups.
metacont 91

byvar Deprecated argument (replaced by ’subgroup’).

keepdata A logical indicating whether original data (set) should be kept in meta object.
warn A logical indicating whether warnings should be printed (e.g., if studies are
excluded from meta-analysis due to zero standard deviations).
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
control An optional list to control the iterative process to estimate the between-study
variance τ 2 . This argument is passed on to rma.uni.
... Additional arguments (to catch deprecated arguments).

Details
Calculation of fixed and random effects estimates for meta-analyses with continuous outcome data;
inverse variance weighting is used for pooling.
Three different types of summary measures are available for continuous outcomes:

• mean difference (argument sm = "MD")

• standardised mean difference (sm = "SMD")
• ratio of means (sm = "ROM")

Default settings are utilised for several arguments (assignments using gs function). These defaults
can be changed for the current R session using the settings.meta function.
Furthermore, R function update.meta can be used to rerun a meta-analysis with different settings.

Standardised mean difference:

For the standardised mean difference three methods are implemented:
• Hedges’ g (default, method.smd = "Hedges") - see Hedges (1981)
• Cohen’s d (method.smd = "Cohen") - see Cohen (1988)
• Glass’ delta (method.smd = "Glass") - see Glass (1976)
Hedges (1981) calculated the exact bias in Cohen’s d which is a ratio of gamma distributions
with the degrees of freedom, i.e. total sample size minus two, as argument. By default (argument
exact.smd = FALSE), an accurate approximation of this bias provided in Hedges (1981) is utilised
for Hedges’ g as well as its standard error; these approximations are also used in RevMan 5.
Following Borenstein et al. (2009) these approximations are not used in the estimation of Cohen’s
d. White and Thomas (2005) argued that approximations are unnecessary with modern software
and accordingly promote to use the exact formulae; this is possible using argument exact.smd =
TRUE. For Hedges’ g the exact formulae are used to calculate the standardised mean difference as
well as the standard error; for Cohen’s d the exact formula is only used to calculate the standard
error. In typical applications (with sample sizes above 10), the differences between using the exact
formulae and the approximation will be minimal.
For Glass’ delta, by default (argument sd.glass = "control"), the standard deviation in the con-
trol group (sd.c) is used in the denominator of the standard mean difference. The standard devi-
ation in the experimental group (sd.e) can be used by specifying sd.glass = "experimental".
92 metacont

Ratio of means:
Meta-analysis of ratio of means – also called response ratios – is described in Hedges et al. (1999)
and Friedrich et al. (2008). Calculations are conducted on the log scale and list elements TE,
TE.fixed, and TE.random contain the logarithm of the ratio of means. In printouts and plots
these values are back transformed if argument backtransf = TRUE.

Approximate means from sample sizes, medians and other statistics:

Missing means in the experimental group (analogously for the control group) can be derived from
1. sample size, median, interquartile range and range (arguments n.e, median.e, q1.e, q3.e,
min.e, and max.e),
2. sample size, median and interquartile range (arguments n.e, median.e, q1.e, and q3.e), or
3. sample size, median and range (arguments n.e, median.e, min.e, and max.e).
By default, methods described in Luo et al. (2018) are utilized (argument method.mean = "Luo"):
• equation (15) if sample size, median, interquartile range and range are available,
• equation (11) if sample size, median and interquartile range are available,
• equation (7) if sample size, median and range are available.
Instead the methods described in Wan et al. (2014) are used if argument method.mean = "Wan"):
• equation (10) if sample size, median, interquartile range and range are available,
• equation (14) if sample size, median and interquartile range are available,
• equation (2) if sample size, median and range are available.
By default, missing means are replaced successively using interquartile ranges and ranges (if
available), interquartile ranges (if available) and finally ranges. Arguments approx.mean.e and
approx.mean.c can be used to overwrite this behaviour for each individual study and treatment
arm:
• use means directly (entry "" in argument approx.mean.e or approx.mean.c);
• median, interquartile range and range ("iqr.range");
• median and interquartile range ("iqr");
• median and range ("range").

Approximate standard deviations from sample sizes, medians and other statistics:
Missing standard deviations in the experimental group (analogously for the control group) can be
derived from
1. sample size, median, interquartile range and range (arguments n.e, median.e, q1.e, q3.e,
min.e, and max.e),
2. sample size, median and interquartile range (arguments n.e, median.e, q1.e and q3.e), or
3. sample size, median and range (arguments n.e, median.e, min.e and max.e).
Wan et al. (2014) describe methods to estimate the standard deviation from the sample size,
median and additional statistics. Shi et al. (2020) provide an improved estimate of the standard
deviation if the interquartile range and range are available in addition to the sample size and
median. Accordingly, equation (11) in Shi et al. (2020) is the default (argument method.sd
= "Shi"), if the median, interquartile range and range are provided. The method by Wan et al.
(2014) is used if argument method.sd = "Wan" and, depending on the sample size, either equation
(12) or (13) is used. If only the interquartile range or range is available, equations (15) / (16) and
(7) / (9) in Wan et al. (2014) are used, respectively.
metacont 93

By default, missing standard deviations are replaced successively using these method, i.e., in-
terquartile ranges and ranges are used before interquartile ranges before ranges. Arguments
approx.sd.e and approx.sd.c can be used to overwrite this default for each individual study
and treatment arms:
• sample size, median, interquartile range and range ("iqr.range");
• sample size, median and interquartile range ("iqr");
• sample size, median and range ("range").

Confidence intervals for individual studies:

For the mean difference (argument sm = "MD"), the confidence interval for individual studies can
be based on the
• standard normal distribution (method.ci = "z", default), or
• t-distribution (method.ci = "t").
Note, this choice does not affect the results of the fixed effect and random effects meta-analysis.

Estimation of between-study variance:

The following methods to estimate the between-study variance τ 2 are available:
• DerSimonian-Laird estimator (method.tau = "DL")
• Paule-Mandel estimator (method.tau = "PM")
• Restricted maximum-likelihood estimator (method.tau = "REML")
• Maximum-likelihood estimator (method.tau = "ML")
• Hunter-Schmidt estimator (method.tau = "HS")
• Sidik-Jonkman estimator (method.tau = "SJ")
• Hedges estimator (method.tau = "HE")
• Empirical Bayes estimator (method.tau = "EB")
See metagen for more information on these estimators.

Confidence interval for the between-study variance:

The following methods to calculate a confidence interval for τ 2 and τ are available.

Argument Method
method.tau.ci = "J" Method by Jackson (2013)
method.tau.ci = "BJ" Method by Biggerstaff and Jackson (2008)
method.tau.ci = "QP" Q-Profile method (Viechtbauer, 2007)
method.tau.ci = "PL" Profile-Likelihood method for three-level meta-analysis model
(Van den Noortgate et al., 2013)

See metagen for more information on these methods. No confidence intervals for τ 2 and τ are
calculated if method.tau.ci = "".

In rare settings with very homogeneous treatment estimates, the Hartung-Knapp variance estimate
can be arbitrarily small resulting in a very narrow confidence interval (Knapp and Hartung, 2003;
Wiksten et al., 2016). In such cases, an ad hoc variance correction has been proposed by utilising
the variance estimate from the classic random effects model with the HK method (Knapp and
Hartung, 2003; IQWiQ, 2020). An alternative approach is to use the wider confidence interval of
classic fixed or random effects meta-analysis and the HK method (Wiksten et al., 2016; Jackson
et al., 2017).
Argument adhoc.hakn can be used to choose the ad hoc method:

Argument Ad hoc method

Exclusion of studies from meta-analysis:

Presentation of meta-analysis results:

Value
An object of class c("metacont","meta") with corresponding print, summary, and forest func-
tions. The object is a list containing the following components:

n.e, mean.e, sd.e,

As defined above.
n.c, mean.c, sd.c,
As defined above.
studlab, exclude, sm, method.ci,
As defined above.
median.e, q1.e, q3.e, min.e, max.e,
As defined above.
median.c, q1.c, q3.c, min.c, max.c,
As defined above.
method.mean, method.sd,
As defined above.
approx.mean.e, approx.sd.e, approx.mean.c, approx.sd.c,
As defined above.
level, level.ma,
As defined above.
fixed, random, As defined above.
overall, overall.hetstat,
As defined above.
pooledvar, method.smd, sd.glass,
As defined above.
hakn, adhoc.hakn, method.tau, method.tau.ci,
As defined above.
tau.preset, TE.tau, method.bias,
As defined above.
tau.common, title, complab, outclab,
As defined above.
label.e, label.c, label.left, label.right,
As defined above.
subgroup, subgroup.name,
As defined above.
print.subgroup.name, sep.subgroup, warn,
As defined above.
TE, seTE Estimated treatment effect and standard error of individual studies.
lower, upper Lower and upper confidence interval limits for individual studies.
statistic, pval
Statistic and p-value for test of treatment effect for individual studies.
w.fixed, w.random
Weight of individual studies (in fixed and random effects model).
TE.fixed, seTE.fixed
Estimated overall treatment effect and standard error (fixed effect model).
96 metacont

lower.fixed, upper.fixed
Lower and upper confidence interval limits (fixed effect model).
statistic.fixed, pval.fixed
Statistic and p-value for test of overall treatment effect (fixed effect model).
TE.random, seTE.random
Estimated overall treatment effect and standard error (random effects model).
lower.random, upper.random
Lower and upper confidence interval limits (random effects model).
statistic.random, pval.random
Statistic and p-value for test of overall treatment effect (random effects model).
prediction, level.predict
As defined above.
seTE.predict Standard error utilised for prediction interval.
lower.predict, upper.predict
Lower and upper limits of prediction interval.
k Number of studies combined in meta-analysis.
Q Heterogeneity statistic Q.
df.Q Degrees of freedom for heterogeneity statistic.
pval.Q P-value of heterogeneity test.
tau2 Between-study variance τ 2 .
se.tau2 Standard error of τ 2 .
lower.tau2, upper.tau2
Lower and upper limit of confidence interval for τ 2 .
tau Square-root of between-study variance τ .
lower.tau, upper.tau
Lower and upper limit of confidence interval for τ .
H Heterogeneity statistic H.
lower.H, upper.H
Lower and upper confidence limit for heterogeneity statistic H.
I2 Heterogeneity statistic I2 .
lower.I2, upper.I2
Lower and upper confidence limit for heterogeneity statistic I2 .
Rb Heterogeneity statistic Rb .
lower.Rb, upper.Rb
Lower and upper confidence limit for heterogeneity statistic Rb .
df.hakn Degrees of freedom for test of treatment effect for Hartung-Knapp method (only
if hakn = TRUE).
method Pooling method: "Inverse".
bylevs Levels of grouping variable - if subgroup is not missing.
TE.fixed.w, seTE.fixed.w
Estimated treatment effect and standard error in subgroups (fixed effect model)
- if subgroup is not missing.
metacont 97

lower.fixed.w, upper.fixed.w
Lower and upper confidence interval limits in subgroups (fixed effect model) -
if subgroup is not missing.
statistic.fixed.w, pval.fixed.w
Statistics and p-values for test of treatment effect in subgroups (fixed effect
model) - if subgroup is not missing.
TE.random.w, seTE.random.w
Estimated treatment effect and standard error in subgroups (random effects model)
- if subgroup is not missing.
lower.random.w, upper.random.w
Lower and upper confidence interval limits in subgroups (random effects model)
- if subgroup is not missing.
statistic.random.w, pval.random.w
Statistics and p-values for test of treatment effect in subgroups (random effects
model) - if subgroup is not missing.
w.fixed.w, w.random.w
Weight of subgroups (in fixed and random effects model) - if subgroup is not
missing.
df.hakn.w Degrees of freedom for test of treatment effect for Hartung-Knapp method in
subgroups - if subgroup is not missing and hakn = TRUE.
n.e.w Number of observations in experimental group in subgroups - if subgroup is not
missing.
n.c.w Number of observations in control group in subgroups - if subgroup is not miss-
ing.
k.w Number of studies combined within subgroups - if subgroup is not missing.
k.all.w Number of all studies in subgroups - if subgroup is not missing.
Q.w.fixed Overall within subgroups heterogeneity statistic Q (based on fixed effect model)
- if subgroup is not missing.
Q.w.random Overall within subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing (only calculated if argument tau.common is
TRUE).
df.Q.w Degrees of freedom for test of overall within subgroups heterogeneity - if subgroup
is not missing.
pval.Q.w.fixed P-value of within subgroups heterogeneity statistic Q (based on fixed effect
model) - if subgroup is not missing.
pval.Q.w.random
P-value of within subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
Q.b.fixed Overall between subgroups heterogeneity statistic Q (based on fixed effect model)
- if subgroup is not missing.
Q.b.random Overall between subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
df.Q.b Degrees of freedom for test of overall between subgroups heterogeneity - if
subgroup is not missing.
98 metacont

pval.Q.b.fixed P-value of between subgroups heterogeneity statistic Q (based on fixed effect

model) - if subgroup is not missing.
pval.Q.b.random
P-value of between subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
tau.w Square-root of between-study variance within subgroups - if subgroup is not
missing.
H.w Heterogeneity statistic H within subgroups - if subgroup is not missing.
lower.H.w, upper.H.w
Lower and upper confidence limit for heterogeneity statistic H within subgroups
- if subgroup is not missing.
I2.w Heterogeneity statistic I2 within subgroups - if subgroup is not missing.
lower.I2.w, upper.I2.w
Lower and upper confidence limit for heterogeneity statistic I2 within subgroups
- if subgroup is not missing.
keepdata As defined above.
data Original data (set) used in function call (if keepdata = TRUE).
subset Information on subset of original data used in meta-analysis (if keepdata =
TRUE).
call Function call.
version Version of R package meta used to create object.

Note
The function metagen is called internally to calculate individual and overall treatment estimates and
standard errors.

Author(s)
Guido Schwarzer <[email protected]>

References
Borenstein M, Hedges LV, Higgins JPT, Rothstein HR (2009): Introduction to Meta-Analysis.
Chichester: Wiley
Cohen J (1988): Statistical Power Analysis for the Behavioral Sciences (second ed.). Lawrence
Erlbaum Associates
Cooper H & Hedges LV (1994): The Handbook of Research Synthesis. Newbury Park, CA: Russell
Sage Foundation
DerSimonian R & Laird N (1986): Meta-analysis in clinical trials. Controlled Clinical Trials, 7,
177–88
Friedrich JO, Adhikari NK, Beyene J (2008): The ratio of means method as an alternative to mean
differences for analyzing continuous outcome variables in meta-analysis: A simulation study. BMC
Medical Research Methodology, 8, 32
metacont 99

Glass G (1976): Primary, secondary, and meta-analysis of research. Educational Researcher, 5,

3–8
Hartung J & Knapp G (2001): On tests of the overall treatment effect in meta-analysis with normally
distributed responses. Statistics in Medicine, 20, 1771–82
Hedges LV (1981): Distribution theory for Glass’s estimator of effect size and related estimators.
Journal of Educational and Behavioral Statistics, 6, 107–28
Hedges LV, Gurevitch J, Curtis PS (1999): The meta-analysis of response ratios in experimental
ecology. Ecology, 80, 1150–6
Higgins JPT, Thompson SG, Spiegelhalter DJ (2009): A re-evaluation of random-effects meta-
analysis. Journal of the Royal Statistical Society: Series A, 172, 137–59
IntHout J, Ioannidis JPA, Borm GF (2014): The Hartung-Knapp-Sidik-Jonkman method for random
effects meta-analysis is straightforward and considerably outperforms the standard DerSimonian-
Laird method. BMC Medical Research Methodology, 14, 25
IQWiG (2020): General Methods: Version 6.0. https://www.iqwig.de/en/about-us/methods/
methods-paper/
Jackson D, Law M, Rücker G, Schwarzer G (2017): The Hartung-Knapp modification for random-
effects meta-analysis: A useful refinement but are there any residual concerns? Statistics in Medicine,
36, 3923–34
Knapp G & Hartung J (2003): Improved tests for a random effects meta-regression with a single
covariate. Statistics in Medicine, 22, 2693–710
Langan D, Higgins JPT, Jackson D, Bowden J, Veroniki AA, Kontopantelis E, et al. (2019): A com-
parison of heterogeneity variance estimators in simulated random-effects meta-analyses. Research
Synthesis Methods, 10, 83–98
Luo D, Wan X, Liu J, Tong T (2018): Optimally estimating the sample mean from the sample
size, median, mid-range, and/or mid-quartile range. Statistical Methods in Medical Research, 27,
1785–805
Review Manager (RevMan) [Computer program]. Version 5.4. The Cochrane Collaboration, 2020
Shi J, Luo D, Weng H, Zeng XT, Lin L, Chu H, Tong T (2020): Optimally estimating the sample
standard deviation from the five-number summary. Research Synthesis Methods, 11, 641–54
Van den Noortgate W, López-López JA, Marín-Martínez F, Sánchez-Meca J (2013): Three-level
meta-analysis of dependent effect sizes. Behavior Research Methods, 45, 576–94
Viechtbauer W (2010): Conducting Meta-Analyses in R with the Metafor Package. Journal of
Statistical Software, 36, 1–48
Wan X, Wang W, Liu J, Tong T (2014): Estimating the sample mean and standard deviation from
the sample size, median, range and/or interquartile range. BMC Medical Research Methodology,
14, 135
White IR, Thomas J (2005): Standardized mean differences in individually-randomized and cluster-
randomized trials, with applications to meta-analysis. Clinical Trials, 2, 141–51
Wiksten A, Rücker G, Schwarzer G (2016): Hartung-Knapp method is not always conservative
compared with fixed-effect meta-analysis. Statistics in Medicine, 35, 2503–15

See Also
update.meta, metabin, metagen
100 metacor

Examples
data(Fleiss1993cont)

# Meta-analysis with Hedges' g as effect measure

#
m1 <- metacont(n.psyc, mean.psyc, sd.psyc, n.cont, mean.cont, sd.cont,
data = Fleiss1993cont, sm = "SMD")
m1
forest(m1)

# Use Cohen's d instead of Hedges' g as effect measure

#
update(m1, method.smd = "Cohen")

# Use Glass' delta instead of Hedges' g as effect measure

#
update(m1, method.smd = "Glass")

# Use Glass' delta based on the standard deviation in the experimental group
#
update(m1, method.smd = "Glass", sd.glass = "experimental")

# Calculate Hedges' g based on exact formulae

#
update(m1, exact.smd = TRUE)

data(amlodipine)
m2 <- metacont(n.amlo, mean.amlo, sqrt(var.amlo), n.plac, mean.plac, sqrt(var.plac),
data = amlodipine, studlab = study)
m2

# Use pooled variance

#
update(m2, pooledvar = TRUE)

# Meta-analysis of response ratios (Hedges et al., 1999)

#
data(woodyplants)
m3 <- metacont(n.elev, mean.elev, sd.elev, n.amb, mean.amb, sd.amb,
data = woodyplants, sm = "ROM")
m3
print(m3, backtransf = FALSE)

metacor Meta-analysis of correlations

Description
Calculation of fixed effect / common effect and random effects estimates for meta-analyses with
correlations; inverse variance weighting is used for pooling.
metacor 101

Usage

metacor(
cor,
n,
studlab,
data = NULL,
subset = NULL,
exclude = NULL,
sm = gs("smcor"),
level = gs("level"),
level.ma = gs("level.ma"),
fixed = gs("fixed"),
random = gs("random") | !is.null(tau.preset),
overall = fixed | random,
overall.hetstat = fixed | random,
hakn = gs("hakn"),
adhoc.hakn = gs("adhoc.hakn"),
method.tau = gs("method.tau"),
method.tau.ci = gs("method.tau.ci"),
tau.preset = NULL,
TE.tau = NULL,
tau.common = gs("tau.common"),
prediction = gs("prediction"),
level.predict = gs("level.predict"),
null.effect = 0,
method.bias = gs("method.bias"),
backtransf = gs("backtransf"),
text.fixed = gs("text.fixed"),
text.random = gs("text.random"),
text.predict = gs("text.predict"),
text.w.fixed = gs("text.w.fixed"),
text.w.random = gs("text.w.random"),
title = gs("title"),
complab = gs("complab"),
outclab = "",
subgroup,
subgroup.name = NULL,
print.subgroup.name = gs("print.subgroup.name"),
sep.subgroup = gs("sep.subgroup"),
test.subgroup = gs("test.subgroup"),
prediction.subgroup = gs("prediction.subgroup"),
byvar,
keepdata = gs("keepdata"),
warn.deprecated = gs("warn.deprecated"),
control = NULL,
...
)
102 metacor

Arguments
cor Correlation.
n Number of observations.
studlab An optional vector with study labels.
data An optional data frame containing the study information, i.e., cor and n.
subset An optional vector specifying a subset of studies to be used.
exclude An optional vector specifying studies to exclude from meta-analysis, however,
to include in printouts and forest plots.
sm A character string indicating which summary measure ("ZCOR" or "COR") is to
be used for pooling of studies.
level The level used to calculate confidence intervals for individual studies.
level.ma The level used to calculate confidence intervals for meta-analysis estimates.
fixed A logical indicating whether a fixed effect / common effect meta-analysis should
be conducted.
random A logical indicating whether a random effects meta-analysis should be con-
ducted.
overall A logical indicating whether overall summaries should be reported. This argu-
ment is useful in a meta-analysis with subgroups if overall results should not be
reported.
overall.hetstat
A logical value indicating whether to print heterogeneity measures for overall
treatment comparisons. This argument is useful in a meta-analysis with sub-
groups if heterogeneity statistics should only be printed on subgroup level.
hakn A logical indicating whether the method by Hartung and Knapp should be used
to adjust test statistics and confidence intervals.
adhoc.hakn A character string indicating whether an ad hoc variance correction should be
applied in the case of an arbitrarily small Hartung-Knapp variance estimate, see
Details.
method.tau A character string indicating which method is used to estimate the between-
study variance τ 2 and its square root τ . Either "DL", "PM", "REML", "ML", "HS",
"SJ", "HE", or "EB", can be abbreviated.
method.tau.ci A character string indicating which method is used to estimate the confidence
interval of τ 2 and τ . Either "QP", "BJ", or "J", or "", can be abbreviated.
tau.preset Prespecified value for the square root of the between-study variance τ 2 .
TE.tau Overall effect used to estimate the between-study variance tau-squared.
tau.common A logical indicating whether tau-squared should be the same across subgroups.
prediction A logical indicating whether a prediction interval should be printed.
level.predict The level used to calculate prediction interval for a new study.
null.effect A numeric value specifying the effect under the null hypothesis.
method.bias A character string indicating which test is to be used. Either "Begg", "Egger",
or "Thompson", can be abbreviated. See function metabias.
metacor 103

backtransf A logical indicating whether results for Fisher’s z transformed correlations (sm
= "ZCOR") should be back transformed in printouts and plots. If TRUE (default),
results will be presented as correlations; otherwise Fisher’s z transformed corre-
lations will be shown.
text.fixed A character string used in printouts and forest plot to label the pooled fixed effect
estimate.
text.random A character string used in printouts and forest plot to label the pooled random
effects estimate.
text.predict A character string used in printouts and forest plot to label the prediction inter-
val.
text.w.fixed A character string used to label weights of fixed effect model.
text.w.random A character string used to label weights of random effects model.
title Title of meta-analysis / systematic review.
complab Comparison label.
outclab Outcome label.
subgroup An optional vector to conduct a meta-analysis with subgroups.
subgroup.name A character string with a name for the subgroup variable.
print.subgroup.name
A logical indicating whether the name of the subgroup variable should be printed
in front of the group labels.
sep.subgroup A character string defining the separator between name of subgroup variable and
subgroup label.
test.subgroup A logical value indicating whether to print results of test for subgroup differ-
ences.
prediction.subgroup
A logical indicating whether prediction intervals should be printed for sub-
groups.
byvar Deprecated argument (replaced by ’subgroup’).
keepdata A logical indicating whether original data (set) should be kept in meta object.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
control An optional list to control the iterative process to estimate the between-study
variance τ 2 . This argument is passed on to rma.uni.
... Additional arguments (to catch deprecated arguments).

Details
Fixed effect and random effects meta-analysis of correlations based either on Fisher’s z transfor-
mation of correlations (sm = "ZCOR") or direct combination of (untransformed) correlations (sm =
"COR") (see Cooper et al., p264-5 and p273-4). Only few statisticians would advocate the use of
untransformed correlations unless sample sizes are very large (see Cooper et al., p265). The arti-
ficial example given below shows that the smallest study gets the largest weight if correlations are
combined directly because the correlation is closest to 1.
104 metacor

Estimation of between-study variance:

Confidence interval for the between-study variance:

The following methods to calculate a confidence interval for τ 2 and τ are available.

Argument Method
method.tau.ci = "J" Method by Jackson
method.tau.ci = "BJ" Method by Biggerstaff and Jackson
method.tau.ci = "QP" Q-Profile method

See metagen for more information on these methods. No confidence intervals for τ 2 and τ are
calculated if method.tau.ci = "".

Hartung-Knapp method:
Hartung and Knapp (2001) and Knapp and Hartung (2003) proposed an alternative method for
random effects meta-analysis based on a refined variance estimator for the treatment estimate.
Simulation studies (Hartung and Knapp, 2001; IntHout et al., 2014; Langan et al., 2019) show
improved coverage probabilities compared to the classic random effects method.
In rare settings with very homogeneous treatment estimates, the Hartung-Knapp variance estimate
can be arbitrarily small resulting in a very narrow confidence interval (Knapp and Hartung, 2003;
Wiksten et al., 2016). In such cases, an ad hoc variance correction has been proposed by utilising
the variance estimate from the classic random effects model with the HK method (Knapp and
Hartung, 2003; IQWiQ, 2020). An alternative approach is to use the wider confidence interval of
classic fixed or random effects meta-analysis and the HK method (Wiksten et al., 2016; Jackson
et al., 2017).
Argument adhoc.hakn can be used to choose the ad hoc method:

Argument Ad hoc method

adhoc.hakn = "" not used
adhoc.hakn = "se" use variance correction if HK standard error is smaller
than standard error from classic random effects
meta-analysis (Knapp and Hartung, 2003)
metacor 105

adhoc.hakn = "iqwig6" use variance correction if HK confidence interval

is narrower than CI from classic random effects model
with DerSimonian-Laird estimator (IQWiG, 2020)
adhoc.hakn = "ci" use wider confidence interval of classic random effects
and HK meta-analysis
(Hybrid method 2 in Jackson et al., 2017)

Exclusion of studies from meta-analysis:

Presentation of meta-analysis results:

Value
An object of class c("metacor","meta") with corresponding print, summary, and forest func-
tions. The object is a list containing the following components:
cor, n, studlab, exclude,
As defined above.
sm, level, level.ma,
As defined above.
fixed, random, As defined above.
hakn, adhoc.hakn, method.tau, method.tau.ci,
As defined above.
tau.preset, TE.tau, method.bias,
As defined above.
method.bias, tau.common, title, complab, outclab,
As defined above.
106 metacor

subgroup, subgroup.name, print.subgroup.name, sep.subgroup

As defined above.
TE, seTE Either Fisher’s z transformation of correlations (sm = "ZCOR") or correlations
(sm="COR") for individual studies.
lower, upper Lower and upper confidence interval limits for individual studies.
zval, pval z-value and p-value for test of effect in individual studies.
w.fixed, w.random
Weight of individual studies (in fixed and random effects model).
TE.fixed, seTE.fixed
Estimated overall effect (Fisher’s z transformation of correlation or correlation)
and standard error (fixed effect model).
lower.fixed, upper.fixed
Lower and upper confidence interval limits (fixed effect model).
statistic.fixed, pval.fixed
z-value and p-value for test of overall effect (fixed effect model).
TE.random, seTE.random
Estimated overall effect (Fisher’s z transformation of correlation or correlation)
and standard error (random effects model).
lower.random, upper.random
Lower and upper confidence interval limits (random effects model).
statistic.random, pval.random
z-value or t-value and corresponding p-value for test of overall effect (random
effects model).
prediction, level.predict
As defined above.
seTE.predict Standard error utilised for prediction interval.
lower.predict, upper.predict
Lower and upper limits of prediction interval.
k Number of studies combined in meta-analysis.
Q Heterogeneity statistic Q.
df.Q Degrees of freedom for heterogeneity statistic.
pval.Q P-value of heterogeneity test.
tau2 Between-study variance τ 2 .
se.tau2 Standard error of τ 2 .
lower.tau2, upper.tau2
Lower and upper limit of confidence interval for τ 2 .
tau Square-root of between-study variance τ .
lower.tau, upper.tau
Lower and upper limit of confidence interval for τ .
H Heterogeneity statistic H.
lower.H, upper.H
Lower and upper confidence limit for heterogeneity statistic H.
metacor 107

I2 Heterogeneity statistic I2 .
lower.I2, upper.I2
Lower and upper confidence limit for heterogeneity statistic I2 .
Rb Heterogeneity statistic Rb .
lower.Rb, upper.Rb
Lower and upper confidence limit for heterogeneity statistic Rb .
df.hakn Degrees of freedom for test of effect for Hartung-Knapp method (only if hakn =
TRUE).
method Pooling method: "Inverse".
bylevs Levels of grouping variable - if subgroup is not missing.
TE.fixed.w, seTE.fixed.w
Estimated effect and standard error in subgroups (fixed effect model) - if subgroup
is not missing.
lower.fixed.w, upper.fixed.w
Lower and upper confidence interval limits in subgroups (fixed effect model) -
if subgroup is not missing.
statistic.fixed.w, pval.fixed.w
z-value and p-value for test of effect in subgroups (fixed effect model) - if
subgroup is not missing.
TE.random.w, seTE.random.w
Estimated effect and standard error in subgroups (random effects model) - if
subgroup is not missing.
lower.random.w, upper.random.w
Lower and upper confidence interval limits in subgroups (random effects model)
- if subgroup is not missing.
statistic.random.w, pval.random.w
z-value or t-value and corresponding p-value for test of effect in subgroups (ran-
dom effects model) - if subgroup is not missing.
w.fixed.w, w.random.w
Weight of subgroups (in fixed and random effects model) - if subgroup is not
missing.
df.hakn.w Degrees of freedom for test of effect for Hartung-Knapp method in subgroups -
if subgroup is not missing and hakn = TRUE.
n.e.w Number of observations in experimental group in subgroups - if subgroup is not
missing.
n.c.w Number of observations in control group in subgroups - if subgroup is not miss-
ing.
k.w Number of studies combined within subgroups - if subgroup is not missing.
k.all.w Number of all studies in subgroups - if subgroup is not missing.
Q.w.fixed Overall within subgroups heterogeneity statistic Q (based on fixed effect model)
- if subgroup is not missing.
Q.w.random Overall within subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing (only calculated if argument tau.common is
TRUE).
108 metacor

df.Q.w Degrees of freedom for test of overall within subgroups heterogeneity - if subgroup
is not missing.
pval.Q.w.fixed P-value of within subgroups heterogeneity statistic Q (based on fixed effect
model) - if subgroup is not missing.
pval.Q.w.random
P-value of within subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
Q.b.fixed Overall between subgroups heterogeneity statistic Q (based on fixed effect model)
- if subgroup is not missing.
Q.b.random Overall between subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
df.Q.b Degrees of freedom for test of overall between subgroups heterogeneity - if
subgroup is not missing.
pval.Q.b.fixed P-value of between subgroups heterogeneity statistic Q (based on fixed effect
model) - if subgroup is not missing.
pval.Q.b.random
P-value of between subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
tau.w Square-root of between-study variance within subgroups - if subgroup is not
missing.
H.w Heterogeneity statistic H within subgroups - if subgroup is not missing.
lower.H.w, upper.H.w
Lower and upper confidence limit for heterogeneity statistic H within subgroups
- if subgroup is not missing.
I2.w Heterogeneity statistic I2 within subgroups - if subgroup is not missing.
lower.I2.w, upper.I2.w
Lower and upper confidence limit for heterogeneity statistic I2 within subgroups
- if subgroup is not missing.
keepdata As defined above.
data Original data (set) used in function call (if keepdata = TRUE).
subset Information on subset of original data used in meta-analysis (if keepdata =
TRUE).
call Function call.
version Version of R package meta used to create object.

Note
The function metagen is called internally to calculate individual and overall treatment estimates and
standard errors.

Author(s)
Guido Schwarzer <[email protected]>
metacor 109

References
Cooper H, Hedges LV, Valentine JC (2009): The Handbook of Research Synthesis and Meta-
Analysis, 2nd Edition. New York: Russell Sage Foundation
DerSimonian R & Laird N (1986): Meta-analysis in clinical trials. Controlled Clinical Trials, 7,
177–88
Hartung J & Knapp G (2001): On tests of the overall treatment effect in meta-analysis with normally
distributed responses. Statistics in Medicine, 20, 1771–82
Higgins JPT, Thompson SG, Spiegelhalter DJ (2009): A re-evaluation of random-effects meta-
analysis. Journal of the Royal Statistical Society: Series A, 172, 137–59
IntHout J, Ioannidis JPA, Borm GF (2014): The Hartung-Knapp-Sidik-Jonkman method for random
effects meta-analysis is straightforward and considerably outperforms the standard DerSimonian-
Laird method. BMC Medical Research Methodology, 14, 25
IQWiG (2020): General Methods: Version 6.0. https://www.iqwig.de/en/about-us/methods/
methods-paper/
Jackson D, Law M, Rücker G, Schwarzer G (2017): The Hartung-Knapp modification for random-
effects meta-analysis: A useful refinement but are there any residual concerns? Statistics in Medicine,
36, 3923–34
Knapp G & Hartung J (2003): Improved tests for a random effects meta-regression with a single
covariate. Statistics in Medicine, 22, 2693–710
Langan D, Higgins JPT, Jackson D, Bowden J, Veroniki AA, Kontopantelis E, et al. (2019): A com-
parison of heterogeneity variance estimators in simulated random-effects meta-analyses. Research
Synthesis Methods, 10, 83–98
Viechtbauer W (2010): Conducting Meta-Analyses in R with the Metafor Package. Journal of
Statistical Software, 36, 1–48
Wiksten A, Rücker G, Schwarzer G (2016): Hartung-Knapp method is not always conservative
compared with fixed-effect meta-analysis. Statistics in Medicine, 35, 2503–15

See Also
update.meta, metacont, metagen, print.meta

Examples
m1 <- metacor(c(0.85, 0.7, 0.95), c(20, 40, 10))

# Print correlations (back transformed from Fisher's z

# transformation)
#
m1

# Print Fisher's z transformed correlations

#
print(m1, backtransf = FALSE)

# Forest plot with back transformed correlations

#
110 metacr

forest(m1)

# Forest plot with Fisher's z transformed correlations

#
forest(m1, backtransf = FALSE)

m2 <- update(m1, sm = "cor")

## Not run:
# Identical forest plots (as back transformation is the identity
# transformation)
forest(m2)
forest(m2, backtransf = FALSE)

## End(Not run)

metacr Meta-analysis of outcome data from Cochrane review

Description
Wrapper function to perform meta-analysis for a single outcome of a Cochrane Intervention review.

Usage
metacr(
x,
comp.no = 1,
outcome.no = 1,
method,
sm,
level = gs("level"),
level.ma = gs("level.ma"),
fixed,
random,
hakn = FALSE,
method.tau = "DL",
method.tau.ci = gs("method.tau.ci"),
tau.common = FALSE,
prediction = gs("prediction"),
level.predict = gs("level.predict"),
swap.events,
logscale,
backtransf = gs("backtransf"),
test.subgroup,
prediction.subgroup = gs("prediction.subgroup"),
metacr 111

text.fixed = gs("text.fixed"),
text.random = gs("text.random"),
text.predict = gs("text.predict"),
text.w.fixed = gs("text.w.fixed"),
text.w.random = gs("text.w.random"),
title,
complab,
outclab,
keepdata = gs("keepdata"),
warn = FALSE,
...
)

Arguments
x An object of class rm5 created by R function read.rm5.
comp.no Comparison number.
outcome.no Outcome number.
method A character string indicating which method is to be used for pooling of studies.
One of "Inverse", "MH", or "Peto", can be abbreviated.
sm A character string indicating which summary measure ("RR", "OR", "RD", "ASD",
"HR", "MD", or "SMD", or "ROM") is to be used for pooling of studies.
level The level used to calculate confidence intervals for individual studies.
level.ma The level used to calculate confidence intervals for pooled estimates.
fixed A logical indicating whether a fixed effect meta-analysis should be conducted.
random A logical indicating whether a random effects meta-analysis should be con-
ducted.
hakn A logical indicating whether the method by Hartung and Knapp should be used
to adjust test statistics and confidence intervals.
method.tau A character string indicating which method is used to estimate the between-
study variance τ 2 and its square root τ . Either "DL", "PM", "REML", "ML", "HS",
"SJ", "HE", or "EB", can be abbreviated.
method.tau.ci A character string indicating which method is used to estimate the confidence
interval of τ 2 and τ . Either "QP", "BJ", or "J", or "", can be abbreviated.
tau.common A logical indicating whether tau-squared should be the same across subgroups.
prediction A logical indicating whether a prediction interval should be printed.
level.predict The level used to calculate prediction interval for a new study.
swap.events A logical indicating whether events and non-events should be interchanged.
logscale A logical indicating whether effect estimates are entered on log-scale.
backtransf A logical indicating whether results should be back transformed in printouts
and plots. If backtransf=TRUE (default), results for sm="OR" are printed as
odds ratios rather than log odds ratios and results for sm="ZCOR" are printed as
correlations rather than Fisher’s z transformed correlations, for example.
112 metacr

test.subgroup A logical value indicating whether to print results of test for subgroup differ-
ences.
prediction.subgroup
A logical indicating whether prediction intervals should be printed for sub-
groups.
text.fixed A character string used in printouts and forest plot to label the pooled fixed effect
estimate.
text.random A character string used in printouts and forest plot to label the pooled random
effects estimate.
text.predict A character string used in printouts and forest plot to label the prediction inter-
val.
text.w.fixed A character string used to label weights of fixed effect model.
text.w.random A character string used to label weights of random effects model.
title Title of meta-analysis / systematic review.
complab Comparison label.
outclab Outcome label.
keepdata A logical indicating whether original data (set) should be kept in meta object.
warn A logical indicating whether warnings should be printed (e.g., if incr is added
to studies with zero cell frequencies).
... Additional arguments (to catch deprecated arguments).

Details
Cochrane Intervention reviews are based on the comparison of two interventions. Each Cochrane In-
tervention review can have a variable number of comparisons. For each comparison, a variable num-
ber of outcomes can be define. For each outcome, a seperate meta-analysis is conducted. Review
Manager 5 (RevMan 5) is the current software used for preparing and maintaining Cochrane Re-
views (https://training.cochrane.org/online-learning/core-software-cochrane-reviews/
revman).
This wrapper function can be used to perform meta-analysis for a single outcome of a Cochrane In-
tervention review. Internally, R functions metabin, metacont, and metagen are called - depending
on the definition of the outcome in RevMan 5.
Note, it is recommended to choose the RevMan 5 settings before executing metacr, i.e., settings.meta("revman5").

Value
An object of class "meta" and "metabin", "metacont", or "metagen" depending on outcome type
utilised in Cochrane Intervention review for selected outcome.

Author(s)
Guido Schwarzer <[email protected]>

References
Review Manager (RevMan) [Computer program]. Version 5.4. The Cochrane Collaboration, 2020
metacum 113

See Also

metabin, metacont, metagen, read.rm5, settings.meta

Examples
# Locate export data file "Fleiss1993_CR.csv"
# in sub-directory of package "meta"
#
filename <- system.file("extdata", "Fleiss1993_CR.csv", package = "meta")
#
Fleiss1993_CR <- read.rm5(filename)

# Choose RevMan 5 settings and store old settings

#
oldset <- settings.meta("revman5", quietly = FALSE)

# Same result as R command example(Fleiss1993bin)

#
metacr(Fleiss1993_CR)

# Same result as R command example(Fleiss1993cont)

#
metacr(Fleiss1993_CR, 1, 2)
forest(metacr(Fleiss1993_CR, 1, 2))

# Change summary measure to RR

#
m1 <- metacr(Fleiss1993_CR)
update(m1, sm="RR")

# Use old settings

#
settings.meta(oldset)

metacum Cumulative meta-analysis

Description

Performs a cumulative meta-analysis.

Usage

metacum(x, pooled, sortvar)

114 metacum

Arguments
x An object of class meta.
pooled A character string indicating whether a fixed effect or random effects model is
used for pooling. Either missing (see Details), "fixed", or "random", can be
abbreviated.
sortvar An optional vector used to sort the individual studies (must be of same length as
x$TE).

Details
A cumulative meta-analysis is performed. Studies are included sequentially as defined by sortvar.
Information from object x is utilised if argument pooled is missing. A fixed effect / common effect
model is assumed (pooled = "fixed") if argument x$fixed is TRUE; a random effects model is
assumed (pooled = "random") if argument x$random is TRUE and x$fixed is FALSE.

Value
An object of class c("metacum","meta") with corresponding print, and forest functions. The
object is a list containing the following components:
TE, seTE Estimated treatment effect and standard error of pooled estimate in cumulative
meta-analyses.
lower, upper Lower and upper confidence interval limits.
statistic Statistic for test of overall effect.
pval P-value for test of overall effect.
studlab Study label describing addition of studies.
w Sum of weights from fixed effect or random effects model.
I2 Heterogeneity statistic I2 .
Rb Heterogeneity statistic Rb .
tau Square-root of between-study variance.
df.hakn Degrees of freedom for test of treatment effect for Hartung-Knapp method (only
if hakn = TRUE).
sm Summary measure.
method Method used for pooling.
k Number of studies combined in meta-analysis.
pooled As defined above.
fixed A logical indicating whether analysis is based on fixed effect model.
random A logical indicating whether analysis is based on random effects model.
TE.fixed, seTE.fixed
Value is NA.
TE.random, seTE.random
Value is NA.
Q Value is NA.
metacum 115

level.ma The level used to calculate confidence intervals for pooled estimates.
hakn A logical indicating whether the method by Hartung and Knapp is used to adjust
test statistics and confidence intervals.
adhoc.hakn A character string indicating whether ad hoc variance correction should be used
for Hartung-Knapp method.
method.tau A character string indicating which method is used to estimate the between-
study variance τ 2 .
tau.preset Prespecified value for the square root of the between-study variance τ 2 .
TE.tau Overall treatment effect used to estimate the between-study variance τ 2 .
n.harmonic.mean
Harmonic mean of number of observations (for back transformation of Freeman-
Tukey Double arcsine transformation).
version Version of R package meta used to create object.

Author(s)
Guido Schwarzer <[email protected]>

References
Cooper H & Hedges LV (1994): The Handbook of Research Synthesis. Newbury Park, CA: Russell
Sage Foundation

metacum(m1, sortvar = study)

metacum(m1, sortvar = 7:1)

m2 <- update(m1, title = "Fleiss1993bin meta-analysis", backtransf = FALSE)

metacum(m2)

data(Fleiss1993cont)
m3 <- metacont(n.psyc, mean.psyc, sd.psyc, n.cont, mean.cont, sd.cont,
data = Fleiss1993cont, sm = "SMD")
metacum(m3)
116 metagen

metagen Generic inverse variance meta-analysis

Description
Fixed effect and random effects meta-analysis based on estimates (e.g. log hazard ratios) and their
standard errors. The inverse variance method is used for pooling.
Three-level random effects meta-analysis (Van den Noortgate et al., 2013) is available by internally
calling rma.mv function from R package metafor (Viechtbauer, 2010).

Usage
metagen(
TE,
seTE,
studlab,
data = NULL,
subset = NULL,
exclude = NULL,
id = NULL,
sm = "",
method.ci = if (missing(df)) "z" else "t",
level = gs("level"),
level.ma = gs("level.ma"),
fixed = gs("fixed"),
random = gs("random") | !is.null(tau.preset),
overall = fixed | random,
overall.hetstat = fixed | random,
hakn = gs("hakn"),
adhoc.hakn = gs("adhoc.hakn"),
method.tau = gs("method.tau"),
method.tau.ci = gs("method.tau.ci"),
tau.preset = NULL,
TE.tau = NULL,
tau.common = gs("tau.common"),
detail.tau = "",
prediction = gs("prediction"),
level.predict = gs("level.predict"),
null.effect = 0,
method.bias = gs("method.bias"),
n.e = NULL,
n.c = NULL,
pval,
df,
lower,
upper,
metagen 117

level.ci = 0.95,
median,
q1,
q3,
min,
max,
method.mean = "Luo",
method.sd = "Shi",
approx.TE,
approx.seTE,
backtransf = gs("backtransf"),
pscale = 1,
irscale = 1,
irunit = "person-years",
text.fixed = gs("text.fixed"),
text.random = gs("text.random"),
text.predict = gs("text.predict"),
text.w.fixed = gs("text.w.fixed"),
text.w.random = gs("text.w.random"),
title = gs("title"),
complab = gs("complab"),
outclab = "",
label.e = gs("label.e"),
label.c = gs("label.c"),
label.left = gs("label.left"),
label.right = gs("label.right"),
subgroup,
subgroup.name = NULL,
print.subgroup.name = gs("print.subgroup.name"),
sep.subgroup = gs("sep.subgroup"),
test.subgroup = gs("test.subgroup"),
prediction.subgroup = gs("prediction.subgroup"),
byvar,
keepdata = gs("keepdata"),
warn = gs("warn"),
warn.deprecated = gs("warn.deprecated"),
control = NULL,
...
)

Arguments
TE Estimate of treatment effect, e.g., log hazard ratio or risk difference.
seTE Standard error of treatment estimate.
studlab An optional vector with study labels.
data An optional data frame containing the study information.
subset An optional vector specifying a subset of studies to be used (see Details).
118 metagen

exclude An optional vector specifying studies to exclude from meta-analysis, however,

to include in printouts and forest plots (see Details).
id An optional vector specifying which estimates come from the same study result-
ing in the use of a three-level meta-analysis model.
sm A character string indicating underlying summary measure, e.g., "RD", "RR",
"OR", "ASD", "HR", "MD", "SMD", or "ROM".
method.ci A character string indicating which method is used to calculate confidence in-
tervals for individual studies, see Details.
level The level used to calculate confidence intervals for individual studies.
level.ma The level used to calculate confidence intervals for meta-analysis estimates.
fixed A logical indicating whether a fixed effect / common effect meta-analysis should
be conducted.
random A logical indicating whether a random effects meta-analysis should be con-
ducted.
overall A logical indicating whether overall summaries should be reported. This argu-
ment is useful in a meta-analysis with subgroups if overall results should not be
reported.
overall.hetstat
A logical value indicating whether to print heterogeneity measures for overall
treatment comparisons. This argument is useful in a meta-analysis with sub-
groups if heterogeneity statistics should only be printed on subgroup level.
hakn A logical indicating whether method by Hartung and Knapp should be used to
adjust test statistics and confidence intervals.
adhoc.hakn A character string indicating whether an ad hoc variance correction should be
applied in the case of an arbitrarily small Hartung-Knapp variance estimate.
Either "", "se", "ci", or "iqwig6" (see Details), can be abbreviated.
method.tau A character string indicating which method is used to estimate the between-
study variance τ 2 and its square root τ . Either "DL", "PM", "REML", "ML", "HS",
"SJ", "HE", or "EB", can be abbreviated.
method.tau.ci A character string indicating which method is used to estimate the confidence
interval of τ 2 and τ . Either "QP", "BJ", "J", "PL", or "", can be abbreviated.
tau.preset Prespecified value for the square root of the between-study variance τ 2 .
TE.tau Overall treatment effect used to estimate the between-study variance tau-squared.
tau.common A logical indicating whether tau-squared should be the same across subgroups.
detail.tau Detail on between-study variance estimate.
prediction A logical indicating whether a prediction interval should be printed.
level.predict The level used to calculate prediction interval for a new study.
null.effect A numeric value specifying the effect under the null hypothesis.
method.bias A character string indicating which test is to be used. Either "Begg", "Egger",
or "Thompson", can be abbreviated. See function metabias.
n.e Number of observations in experimental group (or total sample size in study).
metagen 119

n.c Number of observations in control group.

pval P-value (used to estimate the standard error).
df Degrees of freedom (used in test or to construct confidence interval).
lower Lower limit of confidence interval (used to estimate the standard error).
upper Upper limit of confidence interval (used to estimate the standard error).
level.ci Level of confidence interval.
median Median (used to estimate the treatment effect and standard error).
q1 First quartile (used to estimate the treatment effect and standard error).
q3 Third quartile (used to estimate the treatment effect and standard error).
min Minimum (used to estimate the treatment effect and standard error).
max Maximum (used to estimate the treatment effect and standard error).
method.mean A character string indicating which method to use to approximate the mean from
the median and other statistics (see Details).
method.sd A character string indicating which method to use to approximate the standard
deviation from sample size, median, interquartile range and range (see Details).
approx.TE Approximation method to estimate treatment estimate (see Details).
approx.seTE Approximation method to estimate standard error (see Details).
backtransf A logical indicating whether results should be back transformed in printouts
and plots. If backtransf = TRUE (default), results for sm = "OR" are printed as
odds ratios rather than log odds ratios and results for sm = "ZCOR" are printed as
correlations rather than Fisher’s z transformed correlations, for example.
pscale A numeric giving scaling factor for printing of single event probabilities or risk
differences, i.e. if argument sm is equal to "PLOGIT", "PLN", "PRAW", "PAS",
"PFT", or "RD".
irscale A numeric defining a scaling factor for printing of single incidence rates or in-
cidence rate differences, i.e. if argument sm is equal to "IR", "IRLN", "IRS",
"IRFT", or "IRD".
irunit A character specifying the time unit used to calculate rates, e.g. person-years.
text.fixed A character string used in printouts and forest plot to label the pooled fixed effect
estimate.
text.random A character string used in printouts and forest plot to label the pooled random
effects estimate.
text.predict A character string used in printouts and forest plot to label the prediction inter-
val.
text.w.fixed A character string used to label weights of fixed effect model.
text.w.random A character string used to label weights of random effects model.
title Title of meta-analysis / systematic review.
complab Comparison label.
outclab Outcome label.
label.e Label for experimental group.
120 metagen

label.c Label for control group.

label.left Graph label on left side of forest plot.
label.right Graph label on right side of forest plot.
subgroup An optional vector to conduct a meta-analysis with subgroups.
subgroup.name A character string with a name for the subgroup variable.
print.subgroup.name
A logical indicating whether the name of the subgroup variable should be printed
in front of the group labels.
sep.subgroup A character string defining the separator between name of subgroup variable and
subgroup label.
test.subgroup A logical value indicating whether to print results of test for subgroup differ-
ences.
prediction.subgroup
A logical indicating whether prediction intervals should be printed for sub-
groups.
byvar Deprecated argument (replaced by ’subgroup’).
keepdata A logical indicating whether original data (set) should be kept in meta object.
warn A logical indicating whether warnings should be printed (e.g., if studies are
excluded from meta-analysis due to zero standard errors).
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
control An optional list to control the iterative process to estimate the between-study
variance τ 2 . This argument is passed on to rma.uni or rma.mv.
... Additional arguments (to catch deprecated arguments).

Details
This function provides the generic inverse variance method for meta-analysis which requires treat-
ment estimates and their standard errors (Borenstein et al., 2010). The method is useful, e.g., for
pooling of survival data (using log hazard ratio and standard errors as input). Arguments TE and
seTE can be used to provide treatment estimates and standard errors directly. However, it is possible
to derive these quantities from other information.
Default settings are utilised for several arguments (assignments using gs function). These defaults
can be changed for the current R session using the settings.meta function.
Furthermore, R function update.meta can be used to rerun a meta-analysis with different settings.

Three-level random effects meta-analysis:

A three-level random effects meta-analysis model (Van den Noortgate et al., 2013) is utilized if
argument id is used and at least one study provides more than one estimate. Internally, rma.mv
is called to conduct the analysis and weights.rma.mv with argument type = "rowsum" is used to
calculate random effects weights.

Approximate treatment estimates:

Missing treatment estimates can be derived from
metagen 121

1. confidence limits provided by arguments lower and upper;

2. median, interquartile range and range (arguments median, q1, q3, min, and max);
3. median and interquartile range (arguments median, q1 and q3);
4. median and range (arguments median, min and max).
For confidence limits, the treatment estimate is defined as the center of the confidence interval (on
the log scale for relative effect measures like the odds ratio or hazard ratio).
If the treatment effect is a mean it can be approximated from sample size, median, interquartile
range and range. By default, methods described in Luo et al. (2018) are utilized (argument
method.mean = "Luo"):
• equation (7) if sample size, median and range are available,
• equation (11) if sample size, median and interquartile range are available,
• equation (15) if sample size, median, range and interquartile range are available.
Instead the methods described in Wan et al. (2014) are used if argument method.mean = "Wan"):
• equation (2) if sample size, median and range are available,
• equation (14) if sample size, median and interquartile range are available,
• equation (10) if sample size, median, range and interquartile range are available.
By default, missing treatment estimates are replaced successively using these method, i.e., con-
fidence limits are utilised before interquartile ranges. Argument approx.TE can be used to over-
write this default for each individual study:
• Use treatment estimate directly (entry "" in argument approx.TE);
• confidence limits ("ci" in argument approx.TE);
• median, interquartile range and range ("iqr.range");
• median and interquartile range ("iqr");
• median and range ("range").

Approximate standard errors:

Missing standard errors can be derived from
1. p-value provided by arguments pval and (optional) df;
2. confidence limits (arguments lower, upper, and (optional) df);
3. sample size, median, interquartile range and range (arguments n.e and / or n.c, median, q1,
q3, min, and max);
4. sample size, median and interquartile range (arguments n.e and / or n.c, median, q1 and
q3);
5. sample size, median and range (arguments n.e and / or n.c, median, min and max).
For p-values and confidence limits, calculations are either based on the standard normal or t dis-
tribution if argument df is provided. Furthermore, argument level.ci can be used to provide the
level of the confidence interval.
Wan et al. (2014) describe methods to estimate the standard deviation (and thus the standard
error by deviding the standard deviation with the square root of the sample size) from the sample
size, median and additional statistics. Shi et al. (2020) provide an improved estimate of the
standard deviation if the interquartile range and range are available in addition to the sample size
and median. Accordingly, equation (11) in Shi et al. (2020) is the default (argument method.sd
= "Shi"), if the median, interquartile range and range are provided (arguments median, q1, q3,
122 metagen

min and max). The method by Wan et al. (2014) is used if argument method.sd = "Wan" and,
depending on the sample size, either equation (12) or (13) is used. If only the interquartile range
or range is available, equations (15) / (16) and (7) / (9) in Wan et al. (2014) are used, respectively.
The sample size of individual studies must be provided with arguments n.e and / or n.c. The
total sample size is calculated as n.e + n.c if both arguments are provided.
By default, missing standard errors are replaced successively using these method, e.g., p-value
before confidence limits before interquartile range and range. Argument approx.seTE can be
used to overwrite this default for each individual study:
• Use standard error directly (entry "" in argument approx.seTE);
• p-value ("pval" in argument approx.seTE);
• confidence limits ("ci");
• median, interquartile range and range ("iqr.range");
• median and interquartile range ("iqr");
• median and range ("range").

Confidence intervals for individual studies:

For the mean difference (argument sm = "MD"), the confidence interval for individual studies can
be based on the
• standard normal distribution (method.ci = "z"), or
• t-distribution (method.ci = "t").
By default, the first method is used if argument df is missing and the second method otherwise.
Note, this choice does not affect the results of the fixed effect and random effects meta-analysis.

Estimation of between-study variance:

The following methods are available to estimate the between-study variance τ 2 .

Argument Method
method.tau = "DL" DerSimonian-Laird estimator (DerSimonian and Laird, 1986)
method.tau = "PM" Paule-Mandel estimator (Paule and Mandel, 1982)
method.tau = "REML" Restricted maximum-likelihood estimator (Viechtbauer, 2005)
method.tau = "ML" Maximum-likelihood estimator (Viechtbauer, 2005)
method.tau = "HS" Hunter-Schmidt estimator (Hunter and Schmidt, 2015)
method.tau = "SJ" Sidik-Jonkman estimator (Sidik and Jonkman, 2005)
method.tau = "HE" Hedges estimator (Hedges and Olkin, 1985)
method.tau = "EB" Empirical Bayes estimator (Morris, 1983)

Historically, the DerSimonian-Laird method was the de facto standard to estimate the between-
study variance τ 2 and is still the default in many software packages including Review Manager 5
(RevMan 5) and R package meta. However, its role has been challenged and especially the Paule-
Mandel and REML estimators have been recommended (Veroniki et al., 2016). Accordingly, the
following R command can be used to use the Paule-Mandel estimator in all meta-analyses of the
R session: settings.meta(method.tau = "PM")

Confidence interval for the between-study variance:

The following methods to calculate a confidence interval for τ 2 and τ are available.

Argument Method
metagen 123

method.tau.ci = "J" Method by Jackson (2013)

method.tau.ci = "BJ" Method by Biggerstaff and Jackson (2008)
method.tau.ci = "QP" Q-Profile method (Viechtbauer, 2007)
method.tau.ci = "PL" Profile-Likelihood method for three-level meta-analysis model
(Van den Noortgate et al., 2013)

The first three methods have been recommended by Veroniki et al. (2016). By default, the Jackson
method is used for the DerSimonian-Laird estimator of τ 2 and the Q-profile method for all other
estimators of τ 2 . The Profile-Likelihood method is the only method available for the three-level
meta-analysis model. No confidence intervals for τ 2 and τ are calculated if method.tau.ci = "".

Hartung-Knapp method:
Hartung and Knapp (2001a,b) proposed an alternative method for random effects meta-analysis
based on a refined variance estimator for the treatment estimate. Simulation studies (Hartung and
Knapp, 2001a,b; IntHout et al., 2014; Langan et al., 2019) show improved coverage probabilities
compared to the classic random effects method. However, in rare settings with very homogeneous
treatment estimates, the Hartung-Knapp (HK) variance estimate can be arbitrarily small resulting
in a very narrow confidence interval (Knapp and Hartung, 2003; Wiksten et al., 2016). In such
cases, an ad hoc variance correction has been proposed by utilising the variance estimate from
the classic random effects model with the HK method (Knapp and Hartung, 2003; IQWiQ, 2020).
An alternative approach is to use the wider confidence interval of classic fixed or random effects
meta-analysis and the HK method (Wiksten et al., 2016; Jackson et al., 2017).
Argument adhoc.hakn can be used to choose the ad hoc method:

Argument Ad hoc method

Prediction interval:
A prediction interval for the treatment effect of a new study (Higgins et al., 2009) is calculated if
arguments prediction and random are TRUE. Note, the definition of prediction intervals varies in
the literature. This function implements equation (12) of Higgins et al., (2009) which proposed a
t distribution with K-2 degrees of freedom where K corresponds to the number of studies in the
meta-analysis.

Specify the null hypothesis of test for an overall effect:

124 metagen

Argument null.effect can be used to specify the (treatment) effect under the null hypothesis in
a test for an overall effect.
By default (null.effect = 0), the null hypothesis corresponds to "no difference" (which is ob-
vious for absolute effect measures like the mean difference (sm = "MD") or standardised mean
difference (sm = "SMD")). For relative effect measures, e.g., risk ratio (sm = "RR") or odds ratio
(sm = "OR"), the null effect is defined on the log scale, i.e., ln(RR) = 0 or ln(OR) = 0 which is
equivalent to testing RR = 1 or OR = 1.
Use of argument null.effect is especially useful for summary measures without a "natural" null
effect, i.e., in situations without a second (treatment) group. For example, an overall proportion
of 50% could be tested in the meta-analysis of single proportions with argument null.effect =
0.5.
Note, all tests for an overall effect are two-sided with the alternative hypothesis that the effect is
unequal to null.effect.

Exclusion of studies from meta-analysis:

Arguments subset and exclude can be used to exclude studies from the meta-analysis. Studies
are removed completely from the meta-analysis using argument subset, while excluded studies
are shown in printouts and forest plots using argument exclude (see Examples). Meta-analysis
results are the same for both arguments.

Presentation of meta-analysis results:

Internally, both fixed effect and random effects models are calculated regardless of values choosen
for arguments fixed and random. Accordingly, the estimate for the random effects model can be
extracted from component TE.random of an object of class "meta" even if argument random =
FALSE. However, all functions in R package meta will adequately consider the values for fixed
and random. For example, functions print.meta and forest.meta will not show results for the
random effects model if random = FALSE.
Argument pscale can be used to rescale single proportions or risk differences, e.g. pscale =
1000 means that proportions are expressed as events per 1000 observations. This is useful in
situations with (very) low event probabilities.
Argument irscale can be used to rescale single rates or rate differences, e.g. irscale = 1000
means that rates are expressed as events per 1000 time units, e.g. person-years. This is useful in
situations with (very) low rates. Argument irunit can be used to specify the time unit used in
individual studies (default: "person-years"). This information is printed in summaries and forest
plots if argument irscale is not equal to 1.
Default settings for fixed, random, pscale, irscale, irunit and several other arguments can
be set for the whole R session using settings.meta.

Value
An object of class c("metagen","meta") with corresponding print, summary, and forest func-
tions. The object is a list containing the following components:
TE, seTE, studlab, exclude, n.e, n.c
As defined above.
id, sm, method.ci, level, level.ma,
As defined above.
fixed, random, As defined above.
metagen 125

overall, overall.hetstat,
As defined above.
hakn, adhoc.hakn, method.tau, method.tau.ci,
As defined above.
tau.preset, TE.tau, method.bias,
As defined above.
tau.common, title, complab, outclab,
As defined above.
label.e, label.c, label.left, label.right,
As defined above.
subgroup, subgroup.name,
As defined above.
print.subgroup.name, sep.subgroup, warn,
As defined above.
lower, upper Lower and upper confidence interval limits for individual studies.
statistic, pval
Statistic and p-value for test of treatment effect for individual studies.
w.fixed, w.random
Weight of individual studies (in fixed and random effects model).
TE.fixed, seTE.fixed
Estimated overall treatment effect and standard error (fixed effect model).
lower.fixed, upper.fixed
Lower and upper confidence interval limits (fixed effect model).
statistic.fixed, pval.fixed
Statistic and p-value for test of overall treatment effect (fixed effect model).
TE.random, seTE.random
Estimated overall treatment effect and standard error (random effects model).
lower.random, upper.random
Lower and upper confidence interval limits (random effects model).
statistic.random, pval.random
Statistic and p-value for test of overall treatment effect (random effects model).
prediction, level.predict
As defined above.
seTE.predict Standard error utilised for prediction interval.
lower.predict, upper.predict
Lower and upper limits of prediction interval.
null.effect As defined above.
k Number of studies combined in meta-analysis.
Q Heterogeneity statistic.
df.Q Degrees of freedom for heterogeneity statistic.
pval.Q P-value of heterogeneity test.
tau2 Between-study variance τ 2 .
se.tau2 Standard error of τ 2 .
126 metagen

lower.tau2, upper.tau2
Lower and upper limit of confidence interval for τ 2 .
tau Square-root of between-study variance τ .
lower.tau, upper.tau
Lower and upper limit of confidence interval for τ .
H Heterogeneity statistic H.
lower.H, upper.H
Lower and upper confidence limit for heterogeneity statistic H.
I2 Heterogeneity statistic I2 .
lower.I2, upper.I2
Lower and upper confidence limit for heterogeneity statistic I2 .
Rb Heterogeneity statistic Rb .
lower.Rb, upper.Rb
Lower and upper confidence limit for heterogeneity statistic Rb .
approx.TE, approx.seTE
As defined above.
method Pooling method: "Inverse".
df.hakn Degrees of freedom for test of treatment effect for Hartung-Knapp method (only
if hakn = TRUE).
seTE.hakn Estimated standard error for Hartung-Knapp method (not taking ad hoc variance
correction into account).
seTE.hakn.adhoc
Estimated standard error for Hartung-Knapp method (taking ad hoc variance
correction into account).
bylevs Levels of grouping variable - if subgroup is not missing.
TE.fixed.w, seTE.fixed.w
Estimated treatment effect and standard error in subgroups (fixed effect model)
- if subgroup is not missing.
lower.fixed.w, upper.fixed.w
Lower and upper confidence interval limits in subgroups (fixed effect model) -
if subgroup is not missing.
statistic.fixed.w, pval.fixed.w
Statistics and p-values for test of treatment effect in subgroups (fixed effect
model) - if subgroup is not missing.
TE.random.w, seTE.random.w
Estimated treatment effect and standard error in subgroups (random effects model)
- if subgroup is not missing.
lower.random.w, upper.random.w
Lower and upper confidence interval limits in subgroups (random effects model)
- if subgroup is not missing.
statistic.random.w, pval.random.w
Statistics and p-values for test of treatment effect in subgroups (random effects
model) - if subgroup is not missing.
metagen 127

w.fixed.w, w.random.w
Weight of subgroups (in fixed and random effects model) - if subgroup is not
missing.
df.hakn.w Degrees of freedom for test of treatment effect for Hartung-Knapp method in
subgroups - if subgroup is not missing and hakn = TRUE.
n.harmonic.mean.w
Harmonic mean of number of observations in subgroups (for back transfor-
mation of Freeman-Tukey Double arcsine transformation) - if subgroup is not
missing.
n.e.w Number of observations in experimental group in subgroups - if subgroup is not
missing.
n.c.w Number of observations in control group in subgroups - if subgroup is not miss-
ing.
k.w Number of studies combined within subgroups - if subgroup is not missing.
k.all.w Number of all studies in subgroups - if subgroup is not missing.
Q.w.fixed Overall within subgroups heterogeneity statistic Q (based on fixed effect model)
- if subgroup is not missing.
Q.w.random Overall within subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing (only calculated if argument tau.common is
TRUE).
df.Q.w Degrees of freedom for test of overall within subgroups heterogeneity - if subgroup
is not missing.
pval.Q.w.fixed P-value of within subgroups heterogeneity statistic Q (based on fixed effect
model) - if subgroup is not missing.
pval.Q.w.random
P-value of within subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
Q.b.fixed Overall between subgroups heterogeneity statistic Q (based on fixed effect model)
- if subgroup is not missing.
Q.b.random Overall between subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
df.Q.b Degrees of freedom for test of overall between subgroups heterogeneity - if
subgroup is not missing.
pval.Q.b.fixed P-value of between subgroups heterogeneity statistic Q (based on fixed effect
model) - if subgroup is not missing.
pval.Q.b.random
P-value of between subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
tau.w Square-root of between-study variance within subgroups - if subgroup is not
missing.
H.w Heterogeneity statistic H within subgroups - if subgroup is not missing.
lower.H.w, upper.H.w
Lower and upper confidence limit for heterogeneity statistic H within subgroups
- if subgroup is not missing.
128 metagen

I2.w Heterogeneity statistic I2 within subgroups - if subgroup is not missing.

lower.I2.w, upper.I2.w
Lower and upper confidence limit for heterogeneity statistic I2 within subgroups
- if subgroup is not missing.
keepdata As defined above.
data Original data (set) used in function call (if keepdata = TRUE).
subset Information on subset of original data used in meta-analysis (if keepdata =
TRUE).
call Function call.
version Version of R package meta used to create object.

Note
R function rma.uni from R package metafor (Viechtbauer 2010) is called internally to estimate the
between-study variance τ 2 .

Author(s)
Guido Schwarzer <[email protected]>

References
Biggerstaff BJ, Jackson D (2008): The exact distribution of Cochran’s heterogeneity statistic in
one-way random effects meta-analysis. Statistics in Medicine, 27, 6093–110
Borenstein M, Hedges LV, Higgins JP, Rothstein HR (2010): A basic introduction to fixed-effect
and random-effects models for meta-analysis. Research Synthesis Methods, 1, 97–111
Cooper H & Hedges LV (1994): The Handbook of Research Synthesis. Newbury Park, CA: Russell
Sage Foundation
DerSimonian R & Laird N (1986): Meta-analysis in clinical trials. Controlled Clinical Trials, 7,
177–88
Hedges LV & Olkin I (1985): Statistical methods for meta-analysis. San Diego, CA: Academic
Press
Higgins JPT, Thompson SG, Spiegelhalter DJ (2009): A re-evaluation of random-effects meta-
analysis. Journal of the Royal Statistical Society: Series A, 172, 137–59
Hunter JE & Schmidt FL (2015): Methods of Meta-Analysis: Correcting Error and Bias in Research
Findings (Third edition). Thousand Oaks, CA: Sage
Hartung J, Knapp G (2001a): On tests of the overall treatment effect in meta-analysis with normally
distributed responses. Statistics in Medicine, 20, 1771–82
Hartung J, Knapp G (2001b): A refined method for the meta-analysis of controlled clinical trials
with binary outcome. Statistics in Medicine, 20, 3875–89
IntHout J, Ioannidis JPA, Borm GF (2014): The Hartung-Knapp-Sidik-Jonkman method for random
effects meta-analysis is straightforward and considerably outperforms the standard DerSimonian-
Laird method. BMC Medical Research Methodology, 14, 25
IQWiG (2020): General Methods: Version 6.0. https://www.iqwig.de/en/about-us/methods/
methods-paper/
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Jackson D (2013): Confidence intervals for the between-study variance in random effects meta-
analysis using generalised Cochran heterogeneity statistics. Research Synthesis Methods, 4, 220–
229
Jackson D, Law M, Rücker G, Schwarzer G (2017): The Hartung-Knapp modification for random-
effects meta-analysis: A useful refinement but are there any residual concerns? Statistics in Medicine,
36, 3923–34
Knapp G & Hartung J (2003): Improved tests for a random effects meta-regression with a single
covariate. Statistics in Medicine, 22, 2693–710
Langan D, Higgins JPT, Jackson D, Bowden J, Veroniki AA, Kontopantelis E, et al. (2019): A com-
parison of heterogeneity variance estimators in simulated random-effects meta-analyses. Research
Synthesis Methods, 10, 83–98
Luo D, Wan X, Liu J, Tong T (2018): Optimally estimating the sample mean from the sample
size, median, mid-range, and/or mid-quartile range. Statistical Methods in Medical Research, 27,
1785–805
Morris CN (1983): Parametric empirical Bayes inference: Theory and applications (with discus-
sion). Journal of the American Statistical Association 78, 47–65
Paule RC & Mandel J (1982): Consensus values and weighting factors. Journal of Research of the
National Bureau of Standards, 87, 377–85
Review Manager (RevMan) [Computer program]. Version 5.4. The Cochrane Collaboration, 2020
Shi J, Luo D, Weng H, Zeng X-T, Lin L, Chu H, et al. (2020): Optimally estimating the sample
standard deviation from the five-number summary. Research Synthesis Methods.
Sidik K & Jonkman JN (2005): Simple heterogeneity variance estimation for meta-analysis. Jour-
nal of the Royal Statistical Society: Series C (Applied Statistics), 54, 367–84
Veroniki AA, Jackson D, Viechtbauer W, Bender R, Bowden J, Knapp G, et al. (2016): Methods
to estimate the between-study variance and its uncertainty in meta-analysis. Research Synthesis
Methods, 7, 55–79
Viechtbauer W (2005): Bias and efficiency of meta-analytic variance estimators in the random-
effects model. Journal of Educational and Behavioral Statistics, 30, 261–93
Viechtbauer W (2007): Confidence intervals for the amount of heterogeneity in meta-analysis.
Statistics in Medicine, 26, 37–52
Viechtbauer W (2010): Conducting Meta-Analyses in R with the metafor Package. Journal of
Statistical Software, 36, 1–48
Van den Noortgate W, López-López JA, Marín-Martínez F, Sánchez-Meca J (2013): Three-level
meta-analysis of dependent effect sizes. Behavior Research Methods, 45, 576–94
Wan X, Wang W, Liu J, Tong T (2014): Estimating the sample mean and standard deviation from
the sample size, median, range and/or interquartile range. BMC Medical Research Methodology,
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compared with fixed-effect meta-analysis. Statistics in Medicine, 35, 2503–15

See Also
update.meta, metabin, metacont, print.meta, settings.meta
130 metagen

Examples

data(Fleiss1993bin)
m1 <- metabin(d.asp, n.asp, d.plac, n.plac, study,
data = Fleiss1993bin, sm = "RR", method = "I")
m1

# Identical results using the generic inverse variance method with

# log risk ratio and its standard error:
# Note, argument 'n.e' in metagen() is used to provide the total
# sample size which is calculated from the group sample sizes n.e
# and n.c in meta-analysis m1.
m1.gen <- metagen(TE, seTE, studlab, n.e = n.e + n.c, data = m1, sm = "RR")
m1.gen
forest(m1.gen, leftcols = c("studlab", "n.e", "TE", "seTE"))

# Meta-analysis with prespecified between-study variance

#
metagen(m1$TE, m1$seTE, sm = "RR", tau.preset = sqrt(0.1))

# Meta-analysis of survival data:

#
logHR <- log(c(0.95, 1.5))
selogHR <- c(0.25, 0.35)
metagen(logHR, selogHR, sm = "HR")

# Paule-Mandel method to estimate between-study variance for data

# from Paule & Mandel (1982)
#
average <- c(27.044, 26.022, 26.340, 26.787, 26.796)
variance <- c(0.003, 0.076, 0.464, 0.003, 0.014)
#
metagen(average, sqrt(variance), sm = "MD", method.tau = "PM")

# Conduct meta-analysis using hazard ratios and 95% confidence intervals

#
# Data from Steurer et al. (2006), Analysis 1.1 Overall survival
# https://www.cochranelibrary.com/cdsr/doi/10.1002/14651858.CD004270.pub2/abstract
#
study <- c("FCG on CLL 1996", "Leporrier 2001", "Rai 2000", "Robak 2000")
HR <- c(0.55, 0.92, 0.79, 1.18)
lower.HR <- c(0.28, 0.79, 0.59, 0.64)
upper.HR <- c(1.09, 1.08, 1.05, 2.17)
#
# Input must be log hazard ratios, not hazard ratios
#
metagen(log(HR), lower = log(lower.HR), upper = log(upper.HR),
studlab = study, sm = "HR")

# Exclude MRC-1 and MRC-2 studies from meta-analysis, however,

# show them in printouts and forest plots
#
metabin(d.asp, n.asp, d.plac, n.plac, study,
metainc 131

data = Fleiss1993bin, sm = "RR", method = "I",

exclude = study %in% c("MRC-1", "MRC-2"))
#
# Exclude MRC-1 and MRC-2 studies completely from meta-analysis
#
metabin(d.asp, n.asp, d.plac, n.plac, study,
data = Fleiss1993bin, sm = "RR", method = "I",
subset = !(study %in% c("MRC-1", "MRC-2")))

# Exclude studies with total sample size above 1500

#
metabin(d.asp, n.asp, d.plac, n.plac, study,
data = Fleiss1993bin, sm = "RR", method = "I",
exclude = (n.asp + n.plac) > 1500)

# Exclude studies containing "MRC" in study name

#
metabin(d.asp, n.asp, d.plac, n.plac, study,
data = Fleiss1993bin, sm = "RR", method = "I",
exclude = grep("MRC", study))

# Use both arguments 'subset' and 'exclude'

#
metabin(d.asp, n.asp, d.plac, n.plac, study,
data = Fleiss1993bin, sm = "RR", method = "I",
subset = (n.asp + n.plac) > 1500,
exclude = grep("MRC", study))

metainc Meta-analysis of incidence rates

Description
Calculation of fixed effect and random effects estimates (incidence rate ratio or incidence rate dif-
ference) for meta-analyses with event counts. Mantel-Haenszel, Cochran, inverse variance method,
and generalised linear mixed model (GLMM) are available for pooling. For GLMMs, the rma.glmm
function from R package metafor (Viechtbauer 2010) is called internally.

Usage
metainc(
event.e,
time.e,
event.c,
time.c,
studlab,
data = NULL,
subset = NULL,
132 metainc

exclude = NULL,
method = if (sm == "IRSD") "Inverse" else "MH",
sm = gs("sminc"),
incr = gs("incr"),
allincr = gs("allincr"),
addincr = gs("addincr"),
model.glmm = "UM.FS",
level = gs("level"),
level.ma = gs("level.ma"),
fixed = gs("fixed"),
random = gs("random") | !is.null(tau.preset),
overall = fixed | random,
overall.hetstat = fixed | random,
hakn = gs("hakn"),
adhoc.hakn = gs("adhoc.hakn"),
method.tau = ifelse(!is.na(charmatch(tolower(method), "glmm", nomatch = NA)), "ML",
gs("method.tau")),
method.tau.ci = gs("method.tau.ci"),
tau.preset = NULL,
TE.tau = NULL,
tau.common = gs("tau.common"),
prediction = gs("prediction"),
level.predict = gs("level.predict"),
method.bias = gs("method.bias"),
n.e = NULL,
n.c = NULL,
backtransf = if (sm == "IRSD") FALSE else gs("backtransf"),
irscale = 1,
irunit = "person-years",
text.fixed = gs("text.fixed"),
text.random = gs("text.random"),
text.predict = gs("text.predict"),
text.w.fixed = gs("text.w.fixed"),
text.w.random = gs("text.w.random"),
title = gs("title"),
complab = gs("complab"),
outclab = "",
label.e = gs("label.e"),
label.c = gs("label.c"),
label.left = gs("label.left"),
label.right = gs("label.right"),
subgroup,
subgroup.name = NULL,
print.subgroup.name = gs("print.subgroup.name"),
sep.subgroup = gs("sep.subgroup"),
test.subgroup = gs("test.subgroup"),
prediction.subgroup = gs("prediction.subgroup"),
byvar,
metainc 133

keepdata = gs("keepdata"),
warn = gs("warn"),
warn.deprecated = gs("warn.deprecated"),
control = NULL,
...
)

Arguments
event.e Number of events in experimental group.
time.e Person time at risk in experimental group.
event.c Number of events in control group.
time.c Person time at risk in control group.
studlab An optional vector with study labels.
data An optional data frame containing the study information, i.e., event.e, time.e,
event.c, and time.c.
subset An optional vector specifying a subset of studies to be used.
exclude An optional vector specifying studies to exclude from meta-analysis, however,
to include in printouts and forest plots.
method A character string indicating which method is to be used for pooling of studies.
One of "MH", "Inverse", "Cochran", or "GLMM" can be abbreviated.
sm A character string indicating which summary measure ("IRR", "IRD" or "IRSD")
is to be used for pooling of studies, see Details.
incr A numerical value which is added to each cell frequency for studies with a zero
cell count, see Details.
allincr A logical indicating if incr is added to each cell frequency of all studies if at
least one study has a zero cell count. If FALSE (default), incr is added only to
each cell frequency of studies with a zero cell count.
addincr A logical indicating if incr is added to each cell frequency of all studies irre-
spective of zero cell counts.
model.glmm A character string indicating which GLMM should be used. One of "UM.FS",
"UM.RS", and "CM.EL", see Details.
level The level used to calculate confidence intervals for individual studies.
level.ma The level used to calculate confidence intervals for meta-analysis estimates.
fixed A logical indicating whether a fixed effect / common effect meta-analysis should
be conducted.
random A logical indicating whether a random effects meta-analysis should be con-
ducted.
overall A logical indicating whether overall summaries should be reported. This argu-
ment is useful in a meta-analysis with subgroups if overall results should not be
reported.
134 metainc

overall.hetstat
A logical value indicating whether to print heterogeneity measures for overall
treatment comparisons. This argument is useful in a meta-analysis with sub-
groups if heterogeneity statistics should only be printed on subgroup level.
hakn A logical indicating whether the method by Hartung and Knapp should be used
to adjust test statistics and confidence intervals.
adhoc.hakn A character string indicating whether an ad hoc variance correction should be
applied in the case of an arbitrarily small Hartung-Knapp variance estimate, see
Details.
method.tau A character string indicating which method is used to estimate the between-
study variance τ 2 and its square root τ . Either "DL", "PM", "REML", "ML", "HS",
"SJ", "HE", or "EB", can be abbreviated.
method.tau.ci A character string indicating which method is used to estimate the confidence
interval of τ 2 and τ . Either "QP", "BJ", or "J", or "", can be abbreviated.
tau.preset Prespecified value for the square root of the between-study variance τ 2 .
TE.tau Overall treatment effect used to estimate the between-study variance τ 2 .
tau.common A logical indicating whether tau-squared should be the same across subgroups.
prediction A logical indicating whether a prediction interval should be printed.
level.predict The level used to calculate prediction interval for a new study.
method.bias A character string indicating which test is to be used. Either "Begg", "Egger",
or "Thompson", can be abbreviated. See function metabias.
n.e Number of observations in experimental group (optional).
n.c Number of observations in control group (optional).
backtransf A logical indicating whether results for incidence rate ratio (sm = "IRR") should
be back transformed in printouts and plots. If TRUE (default), results will be
presented as incidence rate ratios; otherwise log incidence rate ratios will be
shown.
irscale A numeric defining a scaling factor for printing of incidence rate differences.
irunit A character string specifying the time unit used to calculate rates, e.g. person-
years.
text.fixed A character string used in printouts and forest plot to label the pooled fixed effect
estimate.
text.random A character string used in printouts and forest plot to label the pooled random
effects estimate.
text.predict A character string used in printouts and forest plot to label the prediction inter-
val.
text.w.fixed A character string used to label weights of fixed effect model.
text.w.random A character string used to label weights of random effects model.
title Title of meta-analysis / systematic review.
complab Comparison label.
outclab Outcome label.
metainc 135

label.e Label for experimental group.

label.c Label for control group.
label.left Graph label on left side of forest plot.
label.right Graph label on right side of forest plot.
subgroup An optional vector to conduct a meta-analysis with subgroups.
subgroup.name A character string with a name for the subgroup variable.
print.subgroup.name
A logical indicating whether the name of the subgroup variable should be printed
in front of the group labels.
sep.subgroup A character string defining the separator between name of subgroup variable and
subgroup label.
test.subgroup A logical value indicating whether to print results of test for subgroup differ-
ences.
prediction.subgroup
A logical indicating whether prediction intervals should be printed for sub-
groups.
byvar Deprecated argument (replaced by ’subgroup’).
keepdata A logical indicating whether original data (set) should be kept in meta object.
warn A logical indicating whether warnings should be printed (e.g., if incr is added
to studies with zero cell frequencies).
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
control An optional list to control the iterative process to estimate the between-study
variance τ 2 . This argument is passed on to rma.uni or rma.glmm, respectively.
... Additional arguments (to catch deprecated arguments).

Details
Calculation of fixed and random effects estimates for meta-analyses comparing two incidence rates.
The following measures of treatment effect are available:
• Incidence Rate Ratio (sm = "IRR")
• Incidence Rate Difference (sm = "IRD")
• Square root transformed Incidence Rate Difference (sm = "IRSD")
Default settings are utilised for several arguments (assignments using gs function). These defaults
can be changed for the current R session using the settings.meta function.
Furthermore, R function update.meta can be used to rerun a meta-analysis with different settings.

Meta-analysis method:
By default, both fixed effect and random effects models are considered (see arguments fixed
and random). If method is "MH" (default), the Mantel-Haenszel method is used to calculate the
fixed effect estimate (Greenland & Robbins, 1985); if method is "Inverse", inverse variance
136 metainc

weighting is used for pooling; if method is "Cochran", the Cochran method is used for pooling
(Bayne-Jones, 1964, Chapter 8).
A distinctive and frequently overlooked advantage of incidence rates is that individual patient
data (IPD) can be extracted from count data. Accordingly, statistical methods for IPD, i.e., gen-
eralised linear mixed models, can be utilised in a meta-analysis of incidence rate ratios (Stijnen
et al., 2010). These methods are available (argument method = "GLMM") by calling the rma.glmm
function from R package metafor internally.
Three different GLMMs are available for meta-analysis of incidence rate ratios using argument
model.glmm (which corresponds to argument model in the rma.glmm function):

1. Poisson regression model with fixed study effects (default)

(model.glmm = "UM.FS", i.e., Unconditional Model - Fixed Study effects)
2. Mixed-effects Poisson regression model with random study effects
(model.glmm = "UM.RS", i.e., Unconditional Model - Random Study effects)
3. Generalised linear mixed model (conditional Poisson-Normal)
(model.glmm = "CM.EL", i.e., Conditional Model - Exact Likelihood)

Details on these three GLMMs as well as additional arguments which can be provided using
argument ’...’ in metainc are described in rma.glmm where you can also find information on
the iterative algorithms used for estimation. Note, regardless of which value is used for argument
model.glmm, results for two different GLMMs are calculated: fixed effect model (with fixed
treatment effect) and random effects model (with random treatment effects).

Continuity correction:
For studies with a zero cell count, by default, 0.5 is added to all cell frequencies of these studies
(argument incr). This continuity correction is used both to calculate individual study results
with confidence limits and to conduct meta-analysis based on the inverse variance method. For
Mantel-Haenszel method, Cochran method, and GLMMs, nothing is added to zero cell counts.
Accordingly, estimates for these methods are not defined if the number of events is zero in all
studies either in the experimental or control group.

Estimation of between-study variance:

Confidence interval for the between-study variance:

The following methods to calculate a confidence interval for τ 2 and τ are available.
metainc 137

Argument Method
method.tau.ci = "J" Method by Jackson
method.tau.ci = "BJ" Method by Biggerstaff and Jackson
method.tau.ci = "QP" Q-Profile method

Argument Ad hoc method

For GLMMs, a method similar to Knapp and Hartung (2003) is implemented, see description of
argument tdist in rma.glmm, and the ad hoc variance correction is not available.
Prediction interval:
A prediction interval for the proportion in a new study (Higgins et al., 2009) is calculated if
arguments prediction and random are TRUE. Note, the definition of prediction intervals varies in
the literature. This function implements equation (12) of Higgins et al., (2009) which proposed a
t distribution with K-2 degrees of freedom where K corresponds to the number of studies in the
meta-analysis.
Subgroup analysis:
Argument subgroup can be used to conduct subgroup analysis for a categorical covariate. The
metareg function can be used instead for more than one categorical covariate or continuous co-
variates.
138 metainc

Exclusion of studies from meta-analysis:

Presentation of meta-analysis results:

Value
An object of class c("metainc","meta") with corresponding print, summary, and forest func-
tions. The object is a list containing the following components:
event.e, time.e, event.c, time.c, studlab, exclude,
As defined above.
sm, method, incr, allincr, addincr, model.glmm, warn,
As defined above.
level, level.ma, fixed, random,
As defined above.
overall, overall.hetstat,
As defined above.
hakn, adhoc.hakn, method.tau, method.tau.ci,
As defined above.
tau.preset, TE.tau, method.bias,
As defined above.
tau.common, title, complab, outclab,
As defined above.
label.e, label.c, label.left, label.right,
As defined above.
subgroup, subgroup.name, print.subgroup.name, sep.subgroup
As defined above.
TE, seTE Estimated treatment effect and standard error of individual studies.
lower, upper Lower and upper confidence interval limits for individual studies.
zval, pval z-value and p-value for test of treatment effect for individual studies.
w.fixed, w.random
Weight of individual studies (in fixed and random effects model).
TE.fixed, seTE.fixed
Estimated overall treatment effect and standard error (fixed effect model).
lower.fixed, upper.fixed
Lower and upper confidence interval limits (fixed effect model).
metainc 139

statistic.fixed, pval.fixed
z-value and p-value for test of overall treatment effect (fixed effect model).
TE.random, seTE.random
Estimated overall treatment effect and standard error (random effects model).
lower.random, upper.random
Lower and upper confidence interval limits (random effects model).
statistic.random, pval.random
z-value or t-value and corresponding p-value for test of overall treatment effect
(random effects model).
prediction, level.predict
As defined above.
seTE.predict Standard error utilised for prediction interval.
lower.predict, upper.predict
Lower and upper limits of prediction interval.
k Number of studies combined in meta-analysis.
Q Heterogeneity statistic Q.
df.Q Degrees of freedom for heterogeneity statistic.
pval.Q P-value of heterogeneity test.
Q.LRT Heterogeneity statistic for likelihood-ratio test (only if method = "GLMM").
df.Q.LRT Degrees of freedom for likelihood-ratio test
pval.Q.LRT P-value of likelihood-ratio test.
tau2 Between-study variance τ 2 .
se.tau2 Standard error of τ 2 .
lower.tau2, upper.tau2
Lower and upper limit of confidence interval for τ 2 .
tau Square-root of between-study variance τ .
lower.tau, upper.tau
Lower and upper limit of confidence interval for τ .
H Heterogeneity statistic H.
lower.H, upper.H
Lower and upper confidence limit for heterogeneity statistic H.
I2 Heterogeneity statistic I2 .
lower.I2, upper.I2
Lower and upper confidence limit for heterogeneity statistic I2 .
Rb Heterogeneity statistic Rb .
lower.Rb, upper.Rb
Lower and upper confidence limit for heterogeneity statistic Rb .
sparse Logical flag indicating if any study included in meta-analysis has any zero cell
frequencies.
incr.event Increment added to number of events.
df.hakn Degrees of freedom for test of treatment effect for Hartung-Knapp method (only
if hakn = TRUE).
140 metainc

k.MH Number of studies combined in meta-analysis using Mantel-Haenszel method.

bylevs Levels of grouping variable - if subgroup is not missing.
TE.fixed.w, seTE.fixed.w
Estimated treatment effect and standard error in subgroups (fixed effect model)
- if subgroup is not missing.
lower.fixed.w, upper.fixed.w
Lower and upper confidence interval limits in subgroups (fixed effect model) -
if subgroup is not missing.
statistic.fixed.w, pval.fixed.w
z-value and p-value for test of treatment effect in subgroups (fixed effect model)
- if subgroup is not missing.
TE.random.w, seTE.random.w
Estimated treatment effect and standard error in subgroups (random effects model)
- if subgroup is not missing.
lower.random.w, upper.random.w
Lower and upper confidence interval limits in subgroups (random effects model)
- if subgroup is not missing.
statistic.random.w, pval.random.w
z-value or t-value and corresponding p-value for test of treatment effect in sub-
groups (random effects model) - if subgroup is not missing.
w.fixed.w, w.random.w
Weight of subgroups (in fixed and random effects model) - if subgroup is not
missing.
df.hakn.w Degrees of freedom for test of treatment effect for Hartung-Knapp method in
subgroups - if subgroup is not missing and hakn = TRUE.
event.e.w Number of events in experimental group in subgroups - if subgroup is not miss-
ing.
time.e.w Total person time in subgroups (experimental group) - if subgroup is not miss-
ing.
n.e.w Number of observations in experimental group in subgroups - if subgroup is not
missing.
event.c.w Number of events in control group in subgroups - if subgroup is not missing.
time.c.w Total person time in subgroups (control group) - if subgroup is not missing.
n.c.w Number of observations in control group in subgroups - if subgroup is not miss-
ing.
k.w Number of studies combined within subgroups - if subgroup is not missing.
k.all.w Number of all studies in subgroups - if subgroup is not missing.
Q.w.fixed Overall within subgroups heterogeneity statistic Q (based on fixed effect model)
- if subgroup is not missing.
Q.w.random Overall within subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing (only calculated if argument tau.common is
TRUE).
df.Q.w Degrees of freedom for test of overall within subgroups heterogeneity - if subgroup
is not missing.
metainc 141

pval.Q.w.fixed P-value of within subgroups heterogeneity statistic Q (based on fixed effect

model) - if subgroup is not missing.
pval.Q.w.random
P-value of within subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
Q.b.fixed Overall between subgroups heterogeneity statistic Q (based on fixed effect model)
- if subgroup is not missing.
Q.b.random Overall between subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
df.Q.b Degrees of freedom for test of overall between subgroups heterogeneity - if
subgroup is not missing.
pval.Q.b.fixed P-value of between subgroups heterogeneity statistic Q (based on fixed effect
model) - if subgroup is not missing.
pval.Q.b.random
P-value of between subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
tau.w Square-root of between-study variance within subgroups - if subgroup is not
missing.
H.w Heterogeneity statistic H within subgroups - if subgroup is not missing.
lower.H.w, upper.H.w
Lower and upper confidence limit for heterogeneity statistic H within subgroups
- if subgroup is not missing.
I2.w Heterogeneity statistic I2 within subgroups - if subgroup is not missing.
lower.I2.w, upper.I2.w
Lower and upper confidence limit for heterogeneity statistic I2 within subgroups
- if subgroup is not missing.
keepdata As defined above.
data Original data (set) used in function call (if keepdata = TRUE).
subset Information on subset of original data used in meta-analysis (if keepdata =
TRUE).
.glmm.fixed GLMM object generated by call of rma.glmm function (fixed effect model).
.glmm.random GLMM object generated by call of rma.glmm function (random effects model).
call Function call.
version Version of R package meta used to create object.
version.metafor
Version of R package metafor used for GLMMs.

Author(s)

Guido Schwarzer <[email protected]>

142 metainc

References
Bayne-Jones S et al. (1964): Smoking and Health: Report of the Advisory Committee to the
Surgeon General of the United States. U-23 Department of Health, Education, and Welfare. Public
Health Service Publication No. 1103.
DerSimonian R & Laird N (1986): Meta-analysis in clinical trials. Controlled Clinical Trials, 7,
177–88
Greenland S & Robins JM (1985): Estimation of a common effect parameter from sparse follow-up
data. Biometrics, 41, 55–68
Higgins JPT, Thompson SG, Spiegelhalter DJ (2009): A re-evaluation of random-effects meta-
analysis. Journal of the Royal Statistical Society: Series A, 172, 137–59
Jackson D, Law M, Rücker G, Schwarzer G (2017): The Hartung-Knapp modification for random-
effects meta-analysis: A useful refinement but are there any residual concerns? Statistics in Medicine,
36, 3923–34
Knapp G & Hartung J (2003): Improved tests for a random effects meta-regression with a single
covariate. Statistics in Medicine, 22, 2693–710
Paule RC & Mandel J (1982): Consensus values and weighting factors. Journal of Research of the
National Bureau of Standards, 87, 377–85
Stijnen T, Hamza TH, Ozdemir P (2010): Random effects meta-analysis of event outcome in the
framework of the generalized linear mixed model with applications in sparse data. Statistics in
Medicine, 29, 3046–67
Viechtbauer W (2010): Conducting Meta-Analyses in R with the Metafor Package. Journal of
Statistical Software, 36, 1–48
Wiksten A, Rücker G, Schwarzer G (2016): Hartung-Knapp method is not always conservative
compared with fixed-effect meta-analysis. Statistics in Medicine, 35, 2503–15

See Also
metabin, update.meta, print.meta

Examples
data(smoking)
m1 <- metainc(d.smokers, py.smokers, d.nonsmokers, py.nonsmokers,
data = smoking, studlab = study)
print(m1, digits = 2)

m2 <- update(m1, method = "Cochran")

print(m2, digits = 2)

data(lungcancer)
m3 <- metainc(d.smokers, py.smokers, d.nonsmokers, py.nonsmokers,
data = lungcancer, studlab = study)
print(m3, digits = 2)

# Redo Cochran meta-analysis with inflated standard errors

#
# All cause mortality
metainf 143

#
TEa <- log((smoking$d.smokers/smoking$py.smokers) /
(smoking$d.nonsmokers/smoking$py.nonsmokers))
seTEa <- sqrt(1 / smoking$d.smokers + 1 / smoking$d.nonsmokers +
2.5 / smoking$d.nonsmokers)
metagen(TEa, seTEa, sm = "IRR", studlab = smoking$study)

# Lung cancer mortality

#
TEl <- log((lungcancer$d.smokers/lungcancer$py.smokers) /
(lungcancer$d.nonsmokers/lungcancer$py.nonsmokers))
seTEl <- sqrt(1 / lungcancer$d.smokers + 1 / lungcancer$d.nonsmokers +
2.25 / lungcancer$d.nonsmokers)
metagen(TEl, seTEl, sm = "IRR", studlab = lungcancer$study)

## Not run:
# Meta-analysis using generalised linear mixed models
# (only if R packages 'metafor' and 'lme4' are available)

# Poisson regression model (fixed study effects)

#
m4 <- metainc(d.smokers, py.smokers, d.nonsmokers, py.nonsmokers,
data = smoking, studlab = study, method = "GLMM")
m4

# Mixed-effects Poisson regression model (random study effects)

#
update(m4, model.glmm = "UM.RS", nAGQ = 1)
#
# Generalised linear mixed model (conditional Poisson-Normal)
#
update(m4, model.glmm = "CM.EL")

## End(Not run)

metainf Influence analysis in meta-analysis using leave-one-out method

Description

Performs an influence analysis. Pooled estimates are calculated omitting one study at a time.

Usage

metainf(x, pooled, sortvar)

144 metainf

Arguments
x An object of class meta.
pooled A character string indicating whether a fixed effect or random effects model is
used for pooling. Either missing (see Details), "fixed" or "random", can be
abbreviated.
sortvar An optional vector used to sort the individual studies (must be of same length as
x$TE).

Details
Performs a influence analysis; pooled estimates are calculated omitting one study at a time. Studies
are sorted according to sortvar.
Information from object x is utilised if argument pooled is missing. A fixed effect model is
assumed (pooled="fixed") if argument x$fixed is TRUE; a random effects model is assumed
(pooled="random") if argument x$random is TRUE and x$fixed is FALSE.

Value
An object of class c("metainf","meta") with corresponding print, and forest functions. The
object is a list containing the following components:
TE, seTE Estimated treatment effect and standard error of pooled estimate in influence
analysis.
lower, upper Lower and upper confidence interval limits.
statistic Statistic for test of overall effect.
pval P-value for test of overall effect.
studlab Study label describing omission of studies.
w Sum of weights from fixed effect or random effects model.
I2 Heterogeneity statistic I2 .
Rb Heterogeneity statistic Rb .
tau Square-root of between-study variance.
df.hakn Degrees of freedom for test of treatment effect for Hartung-Knapp method (only
if hakn = TRUE).
sm Summary measure.
method Method used for pooling.
k Number of studies combined in meta-analysis.
pooled As defined above.
fixed A logical indicating whether analysis is based on fixed effect model.
random A logical indicating whether analysis is based on random effects model.
TE.fixed, seTE.fixed
Value is NA.
TE.random, seTE.random
Value is NA.
metainf 145

Q Value is NA.
level.ma The level used to calculate confidence intervals for pooled estimates.
hakn A logical indicating whether the method by Hartung and Knapp is used to adjust
test statistics and confidence intervals.
adhoc.hakn A character string indicating whether ad hoc variance correction should be used
for Hartung-Knapp method.
method.tau A character string indicating which method is used to estimate the between-
study variance τ 2 .
tau.preset Prespecified value for the square root of the between-study variance τ 2 .
TE.tau Overall treatment effect used to estimate the between-study variance τ 2 .
n.harmonic.mean
Harmonic mean of number of observations (for back transformation of Freeman-
Tukey Double arcsine transformation).
version Version of R package meta used to create object.

Author(s)
Guido Schwarzer <[email protected]>

References
Cooper H & Hedges LV (1994): The Handbook of Research Synthesis. Newbury Park, CA: Russell
Sage Foundation

metainf(m1, sortvar = study)

metainf(m1, sortvar = 7:1)

m2 <- update(m1, title = "Fleiss1993bin meta-analysis", backtransf = FALSE)

metainf(m2)

data(Fleiss1993cont)
m3 <- metacont(n.psyc, mean.psyc, sd.psyc, n.cont, mean.cont, sd.cont,
146 metamean

data = Fleiss1993cont, sm = "SMD")

metainf(m3)

metamean Meta-analysis of single means

Description
Calculation of an overall mean from studies reporting a single mean using the inverse variance
method for pooling; inverse variance weighting is used for pooling.

Usage
metamean(
n,
mean,
sd,
studlab,
data = NULL,
subset = NULL,
exclude = NULL,
median,
q1,
q3,
min,
max,
method.mean = "Luo",
method.sd = "Shi",
approx.mean,
approx.sd,
sm = gs("smmean"),
method.ci = gs("method.ci.cont"),
level = gs("level"),
level.ma = gs("level.ma"),
fixed = gs("fixed"),
random = gs("random") | !is.null(tau.preset),
overall = fixed | random,
overall.hetstat = fixed | random,
hakn = gs("hakn"),
adhoc.hakn = gs("adhoc.hakn"),
method.tau = gs("method.tau"),
method.tau.ci = gs("method.tau.ci"),
tau.preset = NULL,
TE.tau = NULL,
tau.common = gs("tau.common"),
prediction = gs("prediction"),
metamean 147

level.predict = gs("level.predict"),
null.effect = NA,
method.bias = gs("method.bias"),
backtransf = gs("backtransf"),
text.fixed = gs("text.fixed"),
text.random = gs("text.random"),
text.predict = gs("text.predict"),
text.w.fixed = gs("text.w.fixed"),
text.w.random = gs("text.w.random"),
title = gs("title"),
complab = gs("complab"),
outclab = "",
subgroup,
subgroup.name = NULL,
print.subgroup.name = gs("print.subgroup.name"),
sep.subgroup = gs("sep.subgroup"),
test.subgroup = gs("test.subgroup"),
prediction.subgroup = gs("prediction.subgroup"),
byvar,
keepdata = gs("keepdata"),
warn = gs("warn"),
warn.deprecated = gs("warn.deprecated"),
control = NULL,
...
)

Arguments
n Number of observations.
mean Estimated mean.
sd Standard deviation.
studlab An optional vector with study labels.
data An optional data frame containing the study information.
subset An optional vector specifying a subset of studies to be used.
exclude An optional vector specifying studies to exclude from meta-analysis, however,
to include in printouts and forest plots.
median Median (used to estimate the mean and standard deviation).
q1 First quartile (used to estimate the mean and standard deviation).
q3 Third quartile (used to estimate the mean and standard deviation).
min Minimum (used to estimate the mean and standard deviation).
max Maximum (used to estimate the mean and standard deviation).
method.mean A character string indicating which method to use to approximate the mean from
the median and other statistics (see Details).
method.sd A character string indicating which method to use to approximate the standard
deviation from sample size, median, interquartile range and range (see Details).
148 metamean

approx.mean Approximation method to estimate means (see Details).

approx.sd Approximation method to estimate standard deviations (see Details).
sm A character string indicating which summary measure ("MRAW" or "MLN") is to
be used for pooling of studies.
method.ci A character string indicating which method is used to calculate confidence in-
tervals for individual studies, see Details.
level The level used to calculate confidence intervals for individual studies.
level.ma The level used to calculate confidence intervals for meta-analysis estimates.
fixed A logical indicating whether a fixed effect / common effect meta-analysis should
be conducted.
random A logical indicating whether a random effects meta-analysis should be con-
ducted.
overall A logical indicating whether overall summaries should be reported. This argu-
ment is useful in a meta-analysis with subgroups if overall results should not be
reported.
overall.hetstat
A logical value indicating whether to print heterogeneity measures for overall
treatment comparisons. This argument is useful in a meta-analysis with sub-
groups if heterogeneity statistics should only be printed on subgroup level.
hakn A logical indicating whether the method by Hartung and Knapp should be used
to adjust test statistics and confidence intervals.
adhoc.hakn A character string indicating whether an ad hoc variance correction should be
applied in the case of an arbitrarily small Hartung-Knapp variance estimate, see
Details.
method.tau A character string indicating which method is used to estimate the between-
study variance τ 2 and its square root τ . Either "DL", "PM", "REML", "ML", "HS",
"SJ", "HE", or "EB", can be abbreviated.
method.tau.ci A character string indicating which method is used to estimate the confidence
interval of τ 2 and τ . Either "QP", "BJ", or "J", or "", can be abbreviated.
tau.preset Prespecified value for the square root of the between-study variance τ 2 .
TE.tau Overall treatment effect used to estimate the between-study variance tau-squared.
tau.common A logical indicating whether tau-squared should be the same across subgroups.
prediction A logical indicating whether a prediction interval should be printed.
level.predict The level used to calculate prediction interval for a new study.
null.effect A numeric value specifying the effect under the null hypothesis.
method.bias A character string indicating which test is to be used. Either "Begg", "Egger",
or "Thompson", can be abbreviated. See function metabias.
backtransf A logical indicating whether results should be back transformed in printouts
and plots for sm = "MLN". If TRUE (default), results will be presented as means;
otherwise logarithm of means will be shown.
text.fixed A character string used in printouts and forest plot to label the pooled fixed effect
estimate.
metamean 149

text.random A character string used in printouts and forest plot to label the pooled random
effects estimate.
text.predict A character string used in printouts and forest plot to label the prediction inter-
val.
text.w.fixed A character string used to label weights of fixed effect model.
text.w.random A character string used to label weights of random effects model.
title Title of meta-analysis / systematic review.
complab Comparison label.
outclab Outcome label.
subgroup An optional vector to conduct a meta-analysis with subgroups.
subgroup.name A character string with a name for the subgroup variable.
print.subgroup.name
A logical indicating whether the name of the subgroup variable should be printed
in front of the group labels.
sep.subgroup A character string defining the separator between name of subgroup variable and
subgroup label.
test.subgroup A logical value indicating whether to print results of test for subgroup differ-
ences.
prediction.subgroup
A logical indicating whether prediction intervals should be printed for sub-
groups.
byvar Deprecated argument (replaced by ’subgroup’).
keepdata A logical indicating whether original data (set) should be kept in meta object.
warn A logical indicating whether warnings should be printed (e.g., if studies are
excluded from meta-analysis due to zero standard deviations).
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
control An optional list to control the iterative process to estimate the between-study
variance τ 2 . This argument is passed on to rma.uni.
... Additional arguments (to catch deprecated arguments).

Details
Fixed effect and random effects meta-analysis of single means to calculate an overall mean; inverse
variance weighting is used for pooling. The following transformations of means are implemented
to calculate an overall mean:
• Raw, i.e. untransformed, means (sm = "MRAW", default)
• Log transformed means (sm = "MLN")
Note, you should use R function metacont to compare means of pairwise comparisons instead of
using metamean for each treatment arm separately which will break randomisation in randomised
controlled trials.
150 metamean

Calculations are conducted on the log scale if sm = "ROM". Accordingly, list elements TE, TE.fixed,
and TE.random contain the logarithm of means. In printouts and plots these values are back trans-
formed if argument backtransf = TRUE.
Default settings are utilised for several arguments (assignments using gs function). These defaults
can be changed for the current R session using the settings.meta function.
Furthermore, R function update.meta can be used to rerun a meta-analysis with different settings.

Approximate means from sample sizes, medians and other statistics:

Missing means can be derived from
1. sample size, median, interquartile range and range (arguments n, median, q1, q3, min, and
max),
2. sample size, median and interquartile range (arguments n, median, q1, and q3), or
3. sample size, median and range (arguments n, median, min, and max).
By default, methods described in Luo et al. (2018) are utilized (argument method.mean = "Luo"):
• equation (15) if sample size, median, interquartile range and range are available,
• equation (11) if sample size, median and interquartile range are available,
• equation (7) if sample size, median and range are available.
Instead the methods described in Wan et al. (2014) are used if argument method.mean = "Wan"):
• equation (10) if sample size, median, interquartile range and range are available,
• equation (14) if sample size, median and interquartile range are available,
• equation (2) if sample size, median and range are available.
By default, missing means are replaced successively using interquartile ranges and ranges (if
available), interquartile ranges (if available) and finally ranges. Argument approx.mean can be
used to overwrite this behaviour for each individual study and treatment arm:
• use means directly (entry "" in argument approx.mean);
• median, interquartile range and range ("iqr.range");
• median and interquartile range ("iqr");
• median and range ("range").

Approximate standard deviations from sample sizes, medians and other statistics:
Missing standard deviations can be derived from
1. sample size, median, interquartile range and range (arguments n, median, q1, q3, min, and
max),
2. sample size, median and interquartile range (arguments n, median, q1 and q3), or
3. sample size, median and range (arguments n, median, min and max).
Wan et al. (2014) describe methods to estimate the standard deviation from the sample size,
median and additional statistics. Shi et al. (2020) provide an improved estimate of the standard
deviation if the interquartile range and range are available in addition to the sample size and
median. Accordingly, equation (11) in Shi et al. (2020) is the default (argument method.sd
= "Shi"), if the median, interquartile range and range are provided. The method by Wan et al.
(2014) is used if argument method.sd = "Wan" and, depending on the sample size, either equation
(12) or (13) is used. If only the interquartile range or range is available, equations (15) / (16) and
(7) / (9) in Wan et al. (2014) are used, respectively.
metamean 151

By default, missing standard deviations are replaced successively using these method, i.e., in-
terquartile ranges and ranges are used before interquartile ranges before ranges. Argument approx.sd
can be used to overwrite this default for each individual study and treatment arms:
• sample size, median, interquartile range and range ("iqr.range");
• sample size, median and interquartile range ("iqr");
• sample size, median and range ("range").

Confidence intervals for individual studies:

For untransformed means (argument sm = "MRAW"), the confidence interval for individual studies
can be based on the
• standard normal distribution (method.ci = "z", default), or
• t-distribution (method.ci = "t").

Estimation of between-study variance:

Confidence interval for the between-study variance:

The following methods to calculate a confidence interval for τ 2 and τ are available.

Argument Method
method.tau.ci = "J" Method by Jackson
method.tau.ci = "BJ" Method by Biggerstaff and Jackson
method.tau.ci = "QP" Q-Profile method

See metagen for more information on these methods. No confidence intervals for τ 2 and τ are
calculated if method.tau.ci = "".

Hartung-Knapp method:
Hartung and Knapp (2001) proposed an alternative method for random effects meta-analysis based
on a refined variance estimator for the treatment estimate. Simulation studies (Hartung and Knapp,
2001; IntHout et al., 2014; Langan et al., 2019) show improved coverage probabilities compared
to the classic random effects method.
In rare settings with very homogeneous treatment estimates, the Hartung-Knapp variance estimate
can be arbitrarily small resulting in a very narrow confidence interval (Knapp and Hartung, 2003;
Wiksten et al., 2016). In such cases, an ad hoc variance correction has been proposed by utilising
the variance estimate from the classic random effects model with the HK method (Knapp and
152 metamean

Hartung, 2003; IQWiQ, 2020). An alternative approach is to use the wider confidence interval of
classic fixed or random effects meta-analysis and the HK method (Wiksten et al., 2016; Jackson
et al., 2017).
Argument adhoc.hakn can be used to choose the ad hoc method:

Argument Ad hoc method

Exclusion of studies from meta-analysis:

Presentation of meta-analysis results:

Value
An object of class c("metamean","meta") with corresponding print, summary, and forest func-
tions. The object is a list containing the following components:

n, mean, sd, As defined above.

metamean 153

studlab, exclude, sm, method.ci,

As defined above.
median, q1, q3, min, max,
As defined above.
method.mean, method.sd,
As defined above.
approx.mean, approx.sd,
As defined above.
level, level.ma,
As defined above.
fixed, random, As defined above.
overall, overall.hetstat,
As defined above.
hakn, adhoc.hakn, method.tau, method.tau.ci,
As defined above.
tau.preset, TE.tau, method.bias,
As defined above.
tau.common, title, complab, outclab,
As defined above.
subgroup, subgroup.name, print.subgroup.name, sep.subgroup, warn
As defined above.
TE, seTE Estimated effect (mean or log mean) and standard error of individual studies.
lower, upper Lower and upper confidence interval limits for individual studies.
statistic, pval
Statistic and p-value for test of treatment effect for individual studies.
w.fixed, w.random
Weight of individual studies (in fixed and random effects model).
TE.fixed, seTE.fixed
Estimated overall effect (mean or log mean) and standard error (fixed effect
model).
lower.fixed, upper.fixed
Lower and upper confidence interval limits (fixed effect model).
statistic.fixed, pval.fixed
Statistic and p-value for test of overall treatment effect (fixed effect model).
TE.random, seTE.random
Estimated overall effect (mean or log mean) and standard error (random effects
model).
lower.random, upper.random
Lower and upper confidence interval limits (random effects model).
statistic.random, pval.random
Statistic and p-value for test of overall treatment effect (random effects model).
prediction, level.predict
As defined above.
seTE.predict Standard error utilised for prediction interval.
154 metamean

lower.predict, upper.predict
Lower and upper limits of prediction interval.
k Number of studies combined in meta-analysis.
Q Heterogeneity statistic.
tau2 Between-study variance τ 2 .
se.tau2 Standard error of τ 2 .
lower.tau2, upper.tau2
Lower and upper limit of confidence interval for τ 2 .
tau Square-root of between-study variance τ .
lower.tau, upper.tau
Lower and upper limit of confidence interval for τ .
H Heterogeneity statistic H.
lower.H, upper.H
Lower and upper confidence limit for heterogeneity statistic H.
I2 Heterogeneity statistic I2 .
lower.I2, upper.I2
Lower and upper confidence limit for heterogeneity statistic I2 .
Rb Heterogeneity statistic Rb .
lower.Rb, upper.Rb
Lower and upper confidence limit for heterogeneity statistic Rb .
method Pooling method: "Inverse".
df.hakn Degrees of freedom for test of treatment effect for Hartung-Knapp method (only
if hakn = TRUE).
bylevs Levels of grouping variable - if subgroup is not missing.
TE.fixed.w, seTE.fixed.w
Estimated effect and standard error in subgroups (fixed effect model) - if subgroup
is not missing.
lower.fixed.w, upper.fixed.w
Lower and upper confidence interval limits in subgroups (fixed effect model) -
if subgroup is not missing.
statistic.fixed.w, pval.fixed.w
Statistics and p-values for test of treatment effect in subgroups (fixed effect
model) - if subgroup is not missing.
TE.random.w, seTE.random.w
Estimated effect and standard error in subgroups (random effects model) - if
subgroup is not missing.
lower.random.w, upper.random.w
Lower and upper confidence interval limits in subgroups (random effects model)
- if subgroup is not missing.
statistic.random.w, pval.random.w
Statistics and p-values for test of treatment effect in subgroups (random effects
model) - if subgroup is not missing.
metamean 155

w.fixed.w, w.random.w
Weight of subgroups (in fixed and random effects model) - if subgroup is not
missing.
df.hakn.w Degrees of freedom for test of effect for Hartung-Knapp method in subgroups -
if subgroup is not missing and hakn = TRUE.
n.e.w Number of observations in experimental group in subgroups - if subgroup is not
missing.
n.c.w Number of observations in control group in subgroups - if subgroup is not miss-
ing.
k.w Number of studies combined within subgroups - if subgroup is not missing.
k.all.w Number of all studies in subgroups - if subgroup is not missing.
Q.w.fixed Overall within subgroups heterogeneity statistic Q (based on fixed effect model)
- if subgroup is not missing.
Q.w.random Overall within subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing (only calculated if argument tau.common is
TRUE).
df.Q.w Degrees of freedom for test of overall within subgroups heterogeneity - if subgroup
is not missing.
pval.Q.w.fixed P-value of within subgroups heterogeneity statistic Q (based on fixed effect
model) - if subgroup is not missing.
pval.Q.w.random
P-value of within subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
Q.b.fixed Overall between subgroups heterogeneity statistic Q (based on fixed effect model)
- if subgroup is not missing.
Q.b.random Overall between subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
df.Q.b Degrees of freedom for test of overall between subgroups heterogeneity - if
subgroup is not missing.
pval.Q.b.fixed P-value of between subgroups heterogeneity statistic Q (based on fixed effect
model) - if subgroup is not missing.
pval.Q.b.random
P-value of between subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
tau.w Square-root of between-study variance within subgroups - if subgroup is not
missing.
H.w Heterogeneity statistic H within subgroups - if subgroup is not missing.
lower.H.w, upper.H.w
Lower and upper confidence limit for heterogeneity statistic H within subgroups
- if subgroup is not missing.
I2.w Heterogeneity statistic I2 within subgroups - if subgroup is not missing.
lower.I2.w, upper.I2.w
Lower and upper confidence limit for heterogeneity statistic I2 within subgroups
- if subgroup is not missing.
156 metamean

keepdata As defined above.

data Original data (set) used in function call (if keepdata = TRUE).
subset Information on subset of original data used in meta-analysis (if keepdata =
TRUE).
call Function call.
version Version of R package meta used to create object.

Note
The function metagen is called internally to calculate individual and overall treatment estimates and
standard errors.

Author(s)
Guido Schwarzer <[email protected]>

References
DerSimonian R & Laird N (1986): Meta-analysis in clinical trials. Controlled Clinical Trials, 7,
177–88
Hartung J & Knapp G (2001): On tests of the overall treatment effect in meta-analysis with normally
distributed responses. Statistics in Medicine, 20, 1771–82
Higgins JPT, Thompson SG, Spiegelhalter DJ (2009): A re-evaluation of random-effects meta-
analysis. Journal of the Royal Statistical Society: Series A, 172, 137–59
IntHout J, Ioannidis JPA, Borm GF (2014): The Hartung-Knapp-Sidik-Jonkman method for random
effects meta-analysis is straightforward and considerably outperforms the standard DerSimonian-
Laird method. BMC Medical Research Methodology, 14, 25
IQWiG (2020): General Methods: Version 6.0. https://www.iqwig.de/en/about-us/methods/
methods-paper/
Jackson D, Law M, Rücker G, Schwarzer G (2017): The Hartung-Knapp modification for random-
effects meta-analysis: A useful refinement but are there any residual concerns? Statistics in Medicine,
36, 3923–34
Langan D, Higgins JPT, Jackson D, Bowden J, Veroniki AA, Kontopantelis E, et al. (2019): A com-
parison of heterogeneity variance estimators in simulated random-effects meta-analyses. Research
Synthesis Methods, 10, 83–98
Viechtbauer W (2010): Conducting Meta-Analyses in R with the Metafor Package. Journal of
Statistical Software, 36, 1–48
Wiksten A, Rücker G, Schwarzer G (2016): Hartung-Knapp method is not always conservative
compared with fixed-effect meta-analysis. Statistics in Medicine, 35, 2503–15

See Also
update.meta, metamean, metagen
metamerge 157

Examples

m1 <- metamean(rep(100, 3), 1:3, rep(1, 3))

m2 <- update(m1, sm = "MLN")

# With test for overall mean equal to 2

#
update(m1, null.effect = 2)
update(m2, null.effect = 2)

# Print results without back-transformation

#
update(m1, backtransf = FALSE)
update(m2, backtransf = FALSE)
update(m1, null.effect = 2, backtransf = FALSE)
update(m2, null.effect = 2, backtransf = FALSE)

metamerge Merge pooled results of two meta-analyses

Description

This function can be used to merge pooled results of two meta-analyses into a single meta-analysis
object. This is, for example, useful to produce a forest plot of a random-effects meta-analysis with
and without using the Hartung-Knapp method.

Usage

metamerge(
meta1,
meta2,
pooled1,
pooled2,
text.pooled1,
text.pooled2,
text.w.pooled1,
text.w.pooled2,
detail.tau1,
detail.tau2,
backtransf
)
158 metamerge

Arguments
meta1 First meta-analysis object (see Details).
meta2 Second meta-analysis object (see Details).
pooled1 A character string indicating whether results of fixed effect or random effects
model should be considered for first meta-analysis. Either "fixed" or "random",
can be abbreviated.
pooled2 A character string indicating whether results of fixed effect or random effects
model should be considered for second meta-analysis. Either "fixed" or "random",
can be abbreviated.
text.pooled1 A character string used in printouts and forest plot to label the estimate from the
first meta-analysis.
text.pooled2 A character string used in printouts and forest plot to label the estimate from the
second meta-analysis.
text.w.pooled1 A character string used to label weights of the first meta-analysis.
text.w.pooled2 A character string used to label weights of the second meta-analysis.
detail.tau1 A character string used to label estimate of between-study variance of the first
meta-analysis.
detail.tau2 A character string used to label estimate of between-study variance of the second
meta-analysis.
backtransf A logical indicating whether results should be back transformed in printouts and
plots. If backtransf=TRUE (default), results for sm="OR" are printed as odds
ratios rather than log odds ratios, for example.

Details
In R package meta, objects of class "meta" contain results of both a fixed effect and random effects
meta-analysis. This function enables the user to keep the results of one of these models and to add
results from a second meta-analysis or a sensitivity analysis.
Applications of this function include printing and plotting results of the fixed effect or random
effects meta-analysis and the
• Hartung-Knapp method (see argument hakn in metagen),
• trim-and-fill method (trimfill),
• limit meta-analyis (limitmeta from R package metasens),
• Copas selection model (copas from R package metasens),
• robust variance meta-analysis model (robu from R package robumeta).
The first argument must be an object created by a meta-analysis function, e.g., metagen or metabin.
It is also possible to provide an object created with limitmeta or copas. In this case, arguments
meta2 and pooled2 will be ignored.
The second meta-analysis could be an object created by a meta-analysis function or with trimfill,
limitmeta, copas, or robu.
The created meta-analysis object only contains the study results from the first meta-analysis which
are shown in printouts and forest plots. This only makes a difference for meta-analysis methods
metamerge 159

where individual study results differ, e.g., Mantel-Haenszel and Peto method for binary outcomes
(see metabin).
R function metabind can be used to print and plot the results of more than two meta-analyses,
however, without showing individual study results.

Value
An object of class "meta" and "metamerge" with corresponding print, summary, and forest
functions. The following list elements have a different meaning:
TE, seTE, studlab
Treatment estimate, standard error, and study labels (first meta-analyis).
lower, upper Lower and upper confidence interval limits for individual studies (first meta-
analysis).
statistic, pval
Statistic and p-value for test of treatment effect for individual studies (first meta-
analysis.
w.fixed Weight of individual studies (first meta-analysis).
w.random Weight of individual studies (second meta-analysis).
TE.fixed, seTE.fixed
Estimated overall treatment effect and standard error (first meta-analysis).
lower.fixed, upper.fixed
Lower and upper confidence interval limits (first meta-analysis).
statistic.fixed, pval.fixed
Statistic and p-value for test of overall treatment effect (first meta-analysis).
TE.random, seTE.random
Estimated overall treatment effect and standard error (second meta-analysis).
lower.random, upper.random
Lower and upper confidence interval limits (second meta-analysis).
statistic.random, pval.random
Statistic and p-value for test of overall treatment effect (second meta-analysis).
lower.predict, upper.predict
Lower and upper limits of prediction interval (related to first meta-analysis).
k Number of studies combined in first meta-analysis.
Q Heterogeneity statistic (first meta-analysis).
df.Q Degrees of freedom for heterogeneity statistic (first meta-analysis).
pval.Q P-value of heterogeneity test (first meta-analysis).
tau2 Between-study variance(s) τ 2 (first and second meta-analysis).
lower.tau2, upper.tau2
Lower and upper limit of confidence interval(s) for τ 2 (first and second meta-
analysis).
tau Square-root of between-study variance(s) τ (first and second meta-analysis).
lower.tau, upper.tau
Lower and upper limit of confidence interval(s) for τ (first and second meta-
analysis).
160 metamerge

text.fixed Label for the first meta-analysis.

text.random Label for the second meta-analysis.

See metagen for information on other list elements.

Author(s)
Guido Schwarzer <[email protected]>

# Show results for DerSimonian-Laird and REML estimate of

# between-study variance
#
m3 <- update(m1,
text.random = "Random effects moded (DL)", text.w.random = "DL")
m4 <- update(m1, method.tau = "REML",
text.random = "Random effects moded (REML)", text.w.random = "REML")
#
m34 <- metamerge(m3, m4)
m34

data(Fleiss1993bin)
#
# Mantel-Haenszel method
#
m5 <- metabin(d.asp, n.asp, d.plac, n.plac, data = Fleiss1993bin,
studlab = paste(study, year), sm = "OR", random = FALSE,
text.fixed = "MH method", text.w.fixed = "MH")
#
# Peto method
metaprop 161

#
m6 <- update(m5, method = "Peto", text.fixed = "Peto method",
text.w.fixed = "Peto")
#
# Merge results (show individual results for MH method)
#
m56 <- metamerge(m5, m6)
m56
forest(m56, digits = 4)
#
# Merge results (show individual results for Peto method)
#
m65 <- metamerge(m6, m5)
m65

metaprop Meta-analysis of single proportions

Description
Calculation of an overall proportion from studies reporting a single proportion. Inverse variance
method and generalised linear mixed model (GLMM) are available for pooling. For GLMMs, the
rma.glmm function from R package metafor (Viechtbauer 2010) is called internally.

Usage
metaprop(
event,
n,
studlab,
data = NULL,
subset = NULL,
exclude = NULL,
method,
sm = gs("smprop"),
incr = gs("incr"),
allincr = gs("allincr"),
addincr = gs("addincr"),
method.ci = gs("method.ci.prop"),
level = gs("level"),
level.ma = gs("level.ma"),
fixed = gs("fixed"),
random = gs("random") | !is.null(tau.preset),
overall = fixed | random,
overall.hetstat = fixed | random,
hakn = gs("hakn"),
adhoc.hakn = gs("adhoc.hakn"),
162 metaprop

method.tau,
method.tau.ci = gs("method.tau.ci"),
tau.preset = NULL,
TE.tau = NULL,
tau.common = gs("tau.common"),
prediction = gs("prediction"),
level.predict = gs("level.predict"),
null.effect = NA,
method.bias = gs("method.bias"),
backtransf = gs("backtransf"),
pscale = 1,
text.fixed = gs("text.fixed"),
text.random = gs("text.random"),
text.predict = gs("text.predict"),
text.w.fixed = gs("text.w.fixed"),
text.w.random = gs("text.w.random"),
title = gs("title"),
complab = gs("complab"),
outclab = "",
subgroup,
subgroup.name = NULL,
print.subgroup.name = gs("print.subgroup.name"),
sep.subgroup = gs("sep.subgroup"),
test.subgroup = gs("test.subgroup"),
prediction.subgroup = gs("prediction.subgroup"),
byvar,
keepdata = gs("keepdata"),
warn = gs("warn"),
warn.deprecated = gs("warn.deprecated"),
control = NULL,
...
)

Arguments
event Number of events.
n Number of observations.
studlab An optional vector with study labels.
data An optional data frame containing the study information, i.e., event and n.
subset An optional vector specifying a subset of studies to be used.
exclude An optional vector specifying studies to exclude from meta-analysis, however,
to include in printouts and forest plots.
method A character string indicating which method is to be used for pooling of studies.
One of "Inverse" and "GLMM", can be abbreviated.
sm A character string indicating which summary measure ("PLOGIT", "PAS", "PFT",
"PLN", or "PRAW") is to be used for pooling of studies, see Details.
metaprop 163

incr A numeric which is added to event number and sample size of studies with zero
or all events, i.e., studies with an event probability of either 0 or 1.
allincr A logical indicating if incr is considered for all studies if at least one study has
either zero or all events. If FALSE (default), incr is considered only in studies
with zero or all events.
addincr A logical indicating if incr is used for all studies irrespective of number of
events.
method.ci A character string indicating which method is used to calculate confidence in-
tervals for individual studies, see Details.
level The level used to calculate confidence intervals for individual studies.
level.ma The level used to calculate confidence intervals for meta-analysis estimates.
fixed A logical indicating whether a fixed effect / common effect meta-analysis should
be conducted.
random A logical indicating whether a random effects meta-analysis should be con-
ducted.
overall A logical indicating whether overall summaries should be reported. This argu-
ment is useful in a meta-analysis with subgroups if overall results should not be
reported.
overall.hetstat
A logical value indicating whether to print heterogeneity measures for overall
treatment comparisons. This argument is useful in a meta-analysis with sub-
groups if heterogeneity statistics should only be printed on subgroup level.
hakn A logical indicating whether the method by Hartung and Knapp should be used
to adjust test statistics and confidence intervals.
adhoc.hakn A character string indicating whether an ad hoc variance correction should be
applied in the case of an arbitrarily small Hartung-Knapp variance estimate, see
Details.
method.tau A character string indicating which method is used to estimate the between-
study variance τ 2 and its square root τ . Either "DL", "PM", "REML", "ML", "HS",
"SJ", "HE", or "EB", can be abbreviated.
method.tau.ci A character string indicating which method is used to estimate the confidence
interval of τ 2 and τ . Either "QP", "BJ", or "J", or "", can be abbreviated.
tau.preset Prespecified value for the square root of the between-study variance τ 2 .
TE.tau Overall treatment effect used to estimate the between-study variance tau-squared.
tau.common A logical indicating whether tau-squared should be the same across subgroups.
prediction A logical indicating whether a prediction interval should be printed.
level.predict The level used to calculate prediction interval for a new study.
null.effect A numeric value specifying the effect under the null hypothesis.
method.bias A character string indicating which test is to be used. Either "Begg", "Egger",
or "Thompson", can be abbreviated. See function metabias.
backtransf A logical indicating whether results for transformed proportions (argument sm
!= "PRAW") should be back transformed in printouts and plots. If TRUE (de-
fault), results will be presented as proportions; otherwise transformed propor-
tions will be shown. See Details for presentation of confidence intervals.
164 metaprop

pscale A numeric defining a scaling factor for printing of single event probabilities.
text.fixed A character string used in printouts and forest plot to label the pooled fixed effect
estimate.
text.random A character string used in printouts and forest plot to label the pooled random
effects estimate.
text.predict A character string used in printouts and forest plot to label the prediction inter-
val.
text.w.fixed A character string used to label weights of fixed effect model.
text.w.random A character string used to label weights of random effects model.
title Title of meta-analysis / systematic review.
complab Comparison label.
outclab Outcome label.
subgroup An optional vector to conduct a meta-analysis with subgroups.
subgroup.name A character string with a name for the subgroup variable.
print.subgroup.name
A logical indicating whether the name of the subgroup variable should be printed
in front of the group labels.
sep.subgroup A character string defining the separator between name of subgroup variable and
subgroup label.
test.subgroup A logical value indicating whether to print results of test for subgroup differ-
ences.
prediction.subgroup
A logical indicating whether prediction intervals should be printed for sub-
groups.
byvar Deprecated argument (replaced by ’subgroup’).
keepdata A logical indicating whether original data (set) should be kept in meta object.
warn A logical indicating whether the addition of incr to studies with zero or all
events should result in a warning.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
control An optional list to control the iterative process to estimate the between-study
variance τ 2 . This argument is passed on to rma.uni or rma.glmm, respectively.
... Additional arguments passed on to rma.glmm function.

Details
This function provides methods for fixed effect and random effects meta-analysis of single pro-
portions to calculate an overall proportion. Note, you should use R function metabin to compare
proportions of pairwise comparisons instead of using metaprop for each treatment arm separately
which will break randomisation in randomised controlled trials.
The following transformations of proportions are implemented to calculate an overall proportion:
metaprop 165

• Logit transformation (sm = "PLOGIT", default)

• Arcsine transformation (sm = "PAS")
• Freeman-Tukey Double arcsine transformation (sm = "PFT")
• Log transformation (sm = "PLN")
• Raw, i.e. untransformed, proportions (sm = "PRAW")

A generalised linear mixed model (GLMM) - more specific, a random intercept logistic regression
model - can be utilised for the meta-analysis of proportions (Stijnen et al., 2010). This is the default
method for the logit transformation (argument sm = "PLOGIT"). Internally, the rma.glmm function
from R package metafor is called to fit a GLMM.
Classic meta-analysis (Borenstein et al., 2010) utilising the (un)transformed proportions and cor-
responding standard errors in the inverse variance method is conducted by calling the metagen
function internally. This is the only available method for all transformations but the logit trans-
formation. The classic meta-analysis model with logit transformed proportions is used by setting
argument method = "Inverse".
Default settings are utilised for several arguments (assignments using gs function). These defaults
can be changed for the current R session using the settings.meta function.
Furthermore, R function update.meta can be used to rerun a meta-analysis with different settings.

Choice of transformation / meta-analysis method:

Contradictory recommendations on the use of transformations of proportions have been published
in the literature. For example, Barendregt et al. (2013) recommend the use of the Freeman-Tukey
double arcsine transformation instead of the logit transformation whereas Warton & Hui (2011)
strongly advise to use generalised linear mixed models with the logit transformation instead of
the arcsine transformation.
Schwarzer et al. (2019) describe seriously misleading results in a meta-analysis with very different
sample sizes due to problems with the back-transformation of the Freeman-Tukey transformation
which requires a single sample size (Miller, 1978). Accordingly, Schwarzer et al. (2019) also
recommend to use GLMMs for the meta-analysis of single proportions, however, admit that indi-
vidual study weights are not available with this method. Meta-analysts which require individual
study weights should consider the inverse variance method with the arcsine or logit transforma-
tion.
In order to prevent misleading conclusions for the Freeman-Tukey double arcsine transforma-
tion, sensitivity analyses using other transformations or using a range of sample sizes should be
conducted (Schwarzer et al., 2019).

Continuity correction:
If the summary measure is equal to "PLOGIT", "PLN", or "PRAW", a continuity correction is
applied if any study has either zero or all events, i.e., an event probability of either 0 or 1.
By default, 0.5 is used as continuity correction (argument incr). This continuity correction is
used both to calculate individual study results with confidence limits and to conduct meta-analysis
based on the inverse variance method. For GLMMs no continuity correction is used.

Confidence intervals for individual studies:

Various methods are available to calculate confidence intervals for individual study results (see
Agresti & Coull 1998 and Newcombe 1988):
166 metaprop

• Clopper-Pearson interval also called ’exact’ binomial interval (method.ci = "CP", default)
• Wilson Score interval (method.ci = "WS")
• Wilson Score interval with continuity correction (method.ci = "WSCC")
• Agresti-Coull interval (method.ci = "AC")
• Simple approximation interval (method.ci = "SA")
• Simple approximation interval with continuity correction (method.ci = "SACC")
• Normal approximation interval based on summary measure, i.e. defined by argument sm
(method.ci = "NAsm")
Note, with exception of the normal approximation based on the summary measure, i.e. method.ci
= "NAsm", the same confidence interval is calculated for individual studies for any summary mea-
sure (argument sm) as only number of events and observations are used in the calculation disre-
garding the chosen transformation.
Results will be presented for transformed proportions if argument backtransf = FALSE. In this
case, argument method.ci = "NAsm" is used, i.e. confidence intervals based on the normal ap-
proximation based on the summary measure.

Estimation of between-study variance:

Confidence interval for the between-study variance:

The following methods to calculate a confidence interval for τ 2 and τ are available.

Argument Method
method.tau.ci = "J" Method by Jackson
method.tau.ci = "BJ" Method by Biggerstaff and Jackson
method.tau.ci = "QP" Q-Profile method

Knapp, 2001a,b; IntHout et al., 2014; Langan et al., 2019) show improved coverage probabilities
compared to the classic random effects method.
In rare settings with very homogeneous treatment estimates, the Hartung-Knapp variance estimate
can be arbitrarily small resulting in a very narrow confidence interval (Knapp and Hartung, 2003;
Wiksten et al., 2016). In such cases, an ad hoc variance correction has been proposed by utilising
the variance estimate from the classic random effects model with the HK method (Knapp and
Hartung, 2003; IQWiQ, 2020). An alternative approach is to use the wider confidence interval of
classic fixed or random effects meta-analysis and the HK method (Wiksten et al., 2016; Jackson
et al., 2017).
Argument adhoc.hakn can be used to choose the ad hoc method:

Argument Ad hoc method

For GLMMs, a method similar to Knapp and Hartung (2003) is implemented, see description of
argument tdist in rma.glmm, and the ad hoc variance correction is not available.

Specify the null hypothesis of test for an overall proportion:

Argument null.effect can be used to specify the proportion used under the null hypothesis in a
test for an overall effect.
By default (null.effect = NA), no hypothesis test is conducted as it is unclear which value is a
sensible choice for the data at hand. An overall proportion of 50%, for example, could be tested
by setting argument null.effect = 0.5.
Note, all tests for an overall effect are two-sided with the alternative hypothesis that the effect is
unequal to null.effect.

Exclusion of studies from meta-analysis:

168 metaprop

Presentation of meta-analysis results:

Value
An object of class c("metaprop","meta") with corresponding print, summary, and forest func-
tions. The object is a list containing the following components:
event, n, studlab, exclude,
As defined above.
sm, incr, allincr, addincr, method.ci,
As defined above.
level, level.ma,
As defined above.
fixed, random, As defined above.
overall, overall.hetstat,
As defined above.
hakn, adhoc.hakn, method.tau, method.tau.ci,
As defined above.
tau.preset, TE.tau, null.hypothesis,
As defined above.
method.bias, tau.common, title, complab, outclab,
As defined above.
subgroup, subgroup.name, print.subgroup.name, sep.subgroup, warn
As defined above.
TE, seTE Estimated (un)transformed proportion and its standard error for individual stud-
ies.
lower, upper Lower and upper confidence interval limits for individual studies.
zval, pval z-value and p-value for test of treatment effect for individual studies.
w.fixed, w.random
Weight of individual studies (in fixed and random effects model).
TE.fixed, seTE.fixed
Estimated overall (un)transformed proportion and standard error (fixed effect
model).
metaprop 169

lower.fixed, upper.fixed
Lower and upper confidence interval limits (fixed effect model).
statistic.fixed, pval.fixed
z-value and p-value for test of overall effect (fixed effect model).
TE.random, seTE.random
Estimated overall (un)transformed proportion and standard error (random effects
model).
lower.random, upper.random
Lower and upper confidence interval limits (random effects model).
statistic.random, pval.random
z-value or t-value and corresponding p-value for test of overall effect (random
effects model).
prediction, level.predict
As defined above.
seTE.predict Standard error utilised for prediction interval.
lower.predict, upper.predict
Lower and upper limits of prediction interval.
k Number of studies combined in meta-analysis.
Q Heterogeneity statistic Q.
df.Q Degrees of freedom for heterogeneity statistic.
pval.Q P-value of heterogeneity test.
Q.LRT Heterogeneity statistic for likelihood-ratio test (only if method = "GLMM").
df.Q.LRT Degrees of freedom for likelihood-ratio test
pval.Q.LRT P-value of likelihood-ratio test.
tau2 Between-study variance τ 2 .
se.tau2 Standard error of τ 2 .
lower.tau2, upper.tau2
Lower and upper limit of confidence interval for τ 2 .
tau Square-root of between-study variance τ .
lower.tau, upper.tau
Lower and upper limit of confidence interval for τ .
H Heterogeneity statistic H.
lower.H, upper.H
Lower and upper confidence limit for heterogeneity statistic H.
I2 Heterogeneity statistic I2 .
lower.I2, upper.I2
Lower and upper confidence limit for heterogeneity statistic I2 .
Rb Heterogeneity statistic Rb .
lower.Rb, upper.Rb
Lower and upper confidence limit for heterogeneity statistic Rb .
method A character string indicating method used for pooling: "Inverse"
170 metaprop

df.hakn Degrees of freedom for test of treatment effect for Hartung-Knapp method (only
if hakn=TRUE).
bylevs Levels of grouping variable - if subgroup is not missing.
TE.fixed.w, seTE.fixed.w
Estimated treatment effect and standard error in subgroups (fixed effect model)
- if subgroup is not missing.
lower.fixed.w, upper.fixed.w
Lower and upper confidence interval limits in subgroups (fixed effect model) -
if subgroup is not missing.
statistic.fixed.w, pval.fixed.w
z-value and p-value for test of treatment effect in subgroups (fixed effect model)
- if subgroup is not missing.
TE.random.w, seTE.random.w
Estimated treatment effect and standard error in subgroups (random effects model)
- if subgroup is not missing.
lower.random.w, upper.random.w
Lower and upper confidence interval limits in subgroups (random effects model)
- if subgroup is not missing.
statistic.random.w, pval.random.w
z-value or t-value and corresponding p-value for test of treatment effect in sub-
groups (random effects model) - if subgroup is not missing.
w.fixed.w, w.random.w
Weight of subgroups (in fixed and random effects model) - if subgroup is not
missing.
df.hakn.w Degrees of freedom for test of treatment effect for Hartung-Knapp method in
subgroups - if subgroup is not missing and hakn=TRUE.
n.harmonic.mean.w
Harmonic mean of number of observations in subgroups (for back transfor-
mation of Freeman-Tukey Double arcsine transformation) - if subgroup is not
missing.
event.w Number of events in subgroups - if subgroup is not missing.
n.w Number of observations in subgroups - if subgroup is not missing.
k.w Number of studies combined within subgroups - if subgroup is not missing.
k.all.w Number of all studies in subgroups - if subgroup is not missing.
Q.w.fixed Overall within subgroups heterogeneity statistic Q (based on fixed effect model)
- if subgroup is not missing.
Q.w.random Overall within subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing (only calculated if argument tau.common is
TRUE).
df.Q.w Degrees of freedom for test of overall within subgroups heterogeneity - if subgroup
is not missing.
pval.Q.w.fixed P-value of within subgroups heterogeneity statistic Q (based on fixed effect
model) - if subgroup is not missing.
metaprop 171

pval.Q.w.random
P-value of within subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
Q.b.fixed Overall between subgroups heterogeneity statistic Q (based on fixed effect model)
- if subgroup is not missing.
Q.b.random Overall between subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
df.Q.b Degrees of freedom for test of overall between subgroups heterogeneity - if
subgroup is not missing.
pval.Q.b.fixed P-value of between subgroups heterogeneity statistic Q (based on fixed effect
model) - if subgroup is not missing.
pval.Q.b.random
P-value of between subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
tau.w Square-root of between-study variance within subgroups - if subgroup is not
missing.
H.w Heterogeneity statistic H within subgroups - if subgroup is not missing.
lower.H.w, upper.H.w
Lower and upper confidence limit for heterogeneity statistic H within subgroups
- if subgroup is not missing.
I2.w Heterogeneity statistic I2 within subgroups - if subgroup is not missing.
lower.I2.w, upper.I2.w
Lower and upper confidence limit for heterogeneity statistic I2 within subgroups
- if subgroup is not missing.
incr.event Increment added to number of events.
keepdata As defined above.
data Original data (set) used in function call (if keepdata=TRUE).
subset Information on subset of original data used in meta-analysis (if keepdata=TRUE).
.glmm.fixed GLMM object generated by call of rma.glmm function (fixed effect model).
.glmm.random GLMM object generated by call of rma.glmm function (random effects model).
call Function call.
version Version of R package meta used to create object.
version.metafor
Version of R package metafor used for GLMMs.

Author(s)

Guido Schwarzer <[email protected]>

172 metaprop

References
Agresti A & Coull BA (1998): Approximate is better than "exact" for interval estimation of binomial
proportions. The American Statistician, 52, 119–26
Barendregt JJ, Doi SA, Lee YY, Norman RE, Vos T (2013): Meta-analysis of prevalence. Journal
of Epidemiology and Community Health, 67, 974–8
Borenstein M, Hedges LV, Higgins JP, Rothstein HR (2010): A basic introduction to fixed-effect
and random-effects models for meta-analysis. Research Synthesis Methods, 1, 97–111
DerSimonian R & Laird N (1986): Meta-analysis in clinical trials. Controlled Clinical Trials, 7,
177–88
Edward JM et al. (2006): Adherence to antiretroviral therapy in sub-saharan Africa and North
America - a meta-analysis. Journal of the American Medical Association, 296, 679–90
Freeman MF & Tukey JW (1950): Transformations related to the angular and the square root.
Annals of Mathematical Statistics, 21, 607–11
Higgins JPT, Thompson SG, Spiegelhalter DJ (2009): A re-evaluation of random-effects meta-
analysis. Journal of the Royal Statistical Society: Series A, 172, 137–59
Hartung J, Knapp G (2001a): On tests of the overall treatment effect in meta-analysis with normally
distributed responses. Statistics in Medicine, 20, 1771–82
Hartung J, Knapp G (2001b): A refined method for the meta-analysis of controlled clinical trials
with binary outcome. Statistics in Medicine, 20, 3875–89
IntHout J, Ioannidis JPA, Borm GF (2014): The Hartung-Knapp-Sidik-Jonkman method for random
effects meta-analysis is straightforward and considerably outperforms the standard DerSimonian-
Laird method. BMC Medical Research Methodology, 14, 25
IQWiG (2020): General Methods: Version 6.0. https://www.iqwig.de/en/about-us/methods/
methods-paper/
Jackson D, Law M, Rücker G, Schwarzer G (2017): The Hartung-Knapp modification for random-
effects meta-analysis: A useful refinement but are there any residual concerns? Statistics in Medicine,
36, 3923–34
Langan D, Higgins JPT, Jackson D, Bowden J, Veroniki AA, Kontopantelis E, et al. (2019): A com-
parison of heterogeneity variance estimators in simulated random-effects meta-analyses. Research
Synthesis Methods, 10, 83–98
Miller JJ (1978): The inverse of the Freeman-Tukey double arcsine transformation. The American
Statistician, 32, 138
Newcombe RG (1998): Two-sided confidence intervals for the single proportion: comparison of
seven methods. Statistics in Medicine, 17, 857–72
Pettigrew HM, Gart JJ, Thomas DG (1986): The bias and higher cumulants of the logarithm of a
binomial variate. Biometrika, 73, 425–35
Schwarzer G, Chemaitelly H, Abu-Raddad LJ, Rücker G (2019): Seriously misleading results using
inverse of Freeman-Tukey double arcsine transformation in meta-analysis of single proportions.
Research Synthesis Methods, 10, 476–83
Stijnen T, Hamza TH, Ozdemir P (2010): Random effects meta-analysis of event outcome in the
framework of the generalized linear mixed model with applications in sparse data. Statistics in
Medicine, 29, 3046–67
metaprop 173

Viechtbauer W (2010): Conducting meta-analyses in R with the metafor package. Journal of Sta-
tistical Software, 36, 1–48
Warton DI, Hui FKC (2011): The arcsine is asinine: the analysis of proportions in ecology. Ecology,
92, 3–10
Wiksten A, Rücker G, Schwarzer G (2016): Hartung-Knapp method is not always conservative
compared with fixed-effect meta-analysis. Statistics in Medicine, 35, 2503–15

See Also
update.meta, metacont, metagen, print.meta, forest.meta

Examples
# Meta-analysis using generalised linear mixed model
#
metaprop(4:1, 10 * 1:4)

# Apply various classic meta-analysis methods to estimate

# proportions
#
m1 <- metaprop(4:1, 10 * 1:4, method = "Inverse")
m2 <- update(m1, sm = "PAS")
m3 <- update(m1, sm = "PRAW")
m4 <- update(m1, sm = "PLN")
m5 <- update(m1, sm = "PFT")
#
m1
m2
m3
m4
m5
#
forest(m1)
## Not run:
forest(m2)
forest(m3)
forest(m3, pscale = 100)
forest(m4)
forest(m5)

## End(Not run)

# Do not back transform results, e.g. print logit transformed

# proportions if sm = "PLOGIT" and store old settings
#
oldset <- settings.meta(backtransf = FALSE)
#
m6 <- metaprop(4:1, c(10, 20, 30, 40), method = "Inverse")
m7 <- update(m6, sm = "PAS")
m8 <- update(m6, sm = "PRAW")
m9 <- update(m6, sm = "PLN")
m10 <- update(m6, sm = "PFT")
174 metaprop

#
forest(m6)
## Not run:
forest(m7)
forest(m8)
forest(m8, pscale = 100)
forest(m9)
forest(m10)

## End(Not run)

# Use old settings

#
settings.meta(oldset)

# Examples with zero events

#
m1 <- metaprop(c(0, 0, 10, 10), rep(100, 4), method = "Inverse")
m2 <- metaprop(c(0, 0, 10, 10), rep(100, 4), incr = 0.1, method = "Inverse")
#
m1
m2
#
## Not run:
forest(m1)
forest(m2)

## End(Not run)

# Example from Miller (1978):

#
death <- c(3, 6, 10, 1)
animals <- c(11, 17, 21, 6)
#
m3 <- metaprop(death, animals, sm = "PFT")
forest(m3)

# Data examples from Newcombe (1998)

# - apply various methods to estimate confidence intervals for
# individual studies
#
event <- c(81, 15, 0, 1)
n <- c(263, 148, 20, 29)
#
m1 <- metaprop(event, n, method.ci = "SA", method = "Inverse")
m2 <- update(m1, method.ci = "SACC")
m3 <- update(m1, method.ci = "WS")
m4 <- update(m1, method.ci = "WSCC")
m5 <- update(m1, method.ci = "CP")
#
lower <- round(rbind(NA, m1$lower, m2$lower, NA, m3$lower,
m4$lower, NA, m5$lower), 4)
upper <- round(rbind(NA, m1$upper, m2$upper, NA, m3$upper,
metaprop 175

m4$upper, NA, m5$upper), 4)

#
tab1 <- data.frame(
scen1 = meta:::formatCI(lower[, 1], upper[, 1]),
scen2 = meta:::formatCI(lower[, 2], upper[, 2]),
scen3 = meta:::formatCI(lower[, 3], upper[, 3]),
scen4 = meta:::formatCI(lower[, 4], upper[, 4])
)
names(tab1) <- c("r=81, n=263", "r=15, n=148",
"r=0, n=20", "r=1, n=29")
row.names(tab1) <- c("Simple", "- SA", "- SACC",
"Score", "- WS", "- WSCC", "Binomial", "- CP")
tab1[is.na(tab1)] <- ""
# Newcombe (1998), Table I, methods 1-5:
tab1

# Same confidence interval, i.e. unaffected by choice of summary

# measure
#
print(metaprop(event, n, method.ci = "WS", method = "Inverse"), ma = FALSE)
print(metaprop(event, n, sm = "PLN", method.ci = "WS"), ma = FALSE)
print(metaprop(event, n, sm = "PFT", method.ci = "WS"), ma = FALSE)
print(metaprop(event, n, sm = "PAS", method.ci = "WS"), ma = FALSE)
print(metaprop(event, n, sm = "PRAW", method.ci = "WS"), ma = FALSE)

# Different confidence intervals as argument sm = "NAsm"

#
print(metaprop(event, n, method.ci = "NAsm", method = "Inverse"), ma = FALSE)
print(metaprop(event, n, sm = "PLN", method.ci = "NAsm"), ma = FALSE)
print(metaprop(event, n, sm = "PFT", method.ci = "NAsm"), ma = FALSE)
print(metaprop(event, n, sm = "PAS", method.ci = "NAsm"), ma = FALSE)
print(metaprop(event, n, sm = "PRAW", method.ci = "NAsm"), ma = FALSE)

# Different confidence intervals as argument backtransf = FALSE.

# Accordingly, method.ci = "NAsm" used internally.
#
print(metaprop(event, n, method.ci = "WS", method = "Inverse"),
ma = FALSE, backtransf = FALSE)
print(metaprop(event, n, sm = "PLN", method.ci = "WS"),
ma = FALSE, backtransf = FALSE)
print(metaprop(event, n, sm = "PFT", method.ci = "WS"),
ma = FALSE, backtransf = FALSE)
print(metaprop(event, n, sm = "PAS", method.ci = "WS"),
ma = FALSE, backtransf = FALSE)
print(metaprop(event, n, sm = "PRAW", method.ci = "WS"),
ma = FALSE, backtransf = FALSE)

# Same results (printed on original and log scale, respectively)

#
print(metaprop(event, n, sm = "PLN", method.ci = "NAsm"), ma = FALSE)
print(metaprop(event, n, sm = "PLN"), ma = FALSE, backtransf = FALSE)
# Results for first study (on log scale)
round(log(c(0.3079848, 0.2569522, 0.3691529)), 4)
176 metarate

# Print results as events per 1000 observations

#
print(metaprop(6:8, c(100, 1200, 1000), method = "Inverse"),
pscale = 1000, digits = 1)

metarate Meta-analysis of single incidence rates

Description
Calculation of an overall incidence rate from studies reporting a single incidence rate. Inverse vari-
ance method and generalised linear mixed model (GLMM) are available for pooling. For GLMMs,
the rma.glmm function from R package metafor (Viechtbauer 2010) is called internally.

Usage
metarate(
event,
time,
studlab,
data = NULL,
subset = NULL,
exclude = NULL,
n = NULL,
method = "Inverse",
sm = gs("smrate"),
incr = gs("incr"),
allincr = gs("allincr"),
addincr = gs("addincr"),
level = gs("level"),
level.ma = gs("level.ma"),
fixed = gs("fixed"),
random = gs("random") | !is.null(tau.preset),
overall = fixed | random,
overall.hetstat = fixed | random,
hakn = gs("hakn"),
adhoc.hakn = gs("adhoc.hakn"),
method.tau,
method.tau.ci = gs("method.tau.ci"),
tau.preset = NULL,
TE.tau = NULL,
tau.common = gs("tau.common"),
prediction = gs("prediction"),
level.predict = gs("level.predict"),
null.effect = NA,
metarate 177

method.bias = gs("method.bias"),
backtransf = gs("backtransf"),
irscale = 1,
irunit = "person-years",
text.fixed = gs("text.fixed"),
text.random = gs("text.random"),
text.predict = gs("text.predict"),
text.w.fixed = gs("text.w.fixed"),
text.w.random = gs("text.w.random"),
title = gs("title"),
complab = gs("complab"),
outclab = "",
subgroup,
subgroup.name = NULL,
print.subgroup.name = gs("print.subgroup.name"),
sep.subgroup = gs("sep.subgroup"),
test.subgroup = gs("test.subgroup"),
prediction.subgroup = gs("prediction.subgroup"),
byvar,
keepdata = gs("keepdata"),
warn = gs("warn"),
warn.deprecated = gs("warn.deprecated"),
control = NULL,
...
)

Arguments
event Number of events.
time Person time at risk.
studlab An optional vector with study labels.
data An optional data frame containing the study information, i.e., event and time.
subset An optional vector specifying a subset of studies to be used.
exclude An optional vector specifying studies to exclude from meta-analysis, however,
to include in printouts and forest plots.
n Number of observations.
method A character string indicating which method is to be used for pooling of studies.
One of "Inverse" and "GLMM", can be abbreviated.
sm A character string indicating which summary measure ("IR", "IRLN", "IRS", or
"IRFT") is to be used for pooling of studies, see Details.
incr A numeric which is added to the event number of studies with zero events, i.e.,
studies with an incidence rate of 0.
allincr A logical indicating if incr is considered for all studies if at least one study has
zero events. If FALSE (default), incr is considered only in studies with zero
events.
178 metarate

addincr A logical indicating if incr is used for all studies irrespective of number of
events.
level The level used to calculate confidence intervals for individual studies.
level.ma The level used to calculate confidence intervals for meta-analysis estimates.
fixed A logical indicating whether a fixed effect / common effect meta-analysis should
be conducted.
random A logical indicating whether a random effects meta-analysis should be con-
ducted.
overall A logical indicating whether overall summaries should be reported. This argu-
ment is useful in a meta-analysis with subgroups if overall results should not be
reported.
overall.hetstat
A logical value indicating whether to print heterogeneity measures for overall
treatment comparisons. This argument is useful in a meta-analysis with sub-
groups if heterogeneity statistics should only be printed on subgroup level.
hakn A logical indicating whether the method by Hartung and Knapp should be used
to adjust test statistics and confidence intervals.
adhoc.hakn A character string indicating whether an ad hoc variance correction should be
applied in the case of an arbitrarily small Hartung-Knapp variance estimate, see
Details.
method.tau A character string indicating which method is used to estimate the between-
study variance τ 2 and its square root τ . Either "DL", "PM", "REML", "ML", "HS",
"SJ", "HE", or "EB", can be abbreviated.
method.tau.ci A character string indicating which method is used to estimate the confidence
interval of τ 2 and τ . Either "QP", "BJ", or "J", or "", can be abbreviated.
tau.preset Prespecified value for the square root of the between-study variance τ 2 .
TE.tau Overall treatment effect used to estimate the between-study variance tau-squared.
tau.common A logical indicating whether tau-squared should be the same across subgroups.
prediction A logical indicating whether a prediction interval should be printed.
level.predict The level used to calculate prediction interval for a new study.
null.effect A numeric value specifying the effect under the null hypothesis.
method.bias A character string indicating which test is to be used. Either "Begg", "Egger",
or "Thompson", can be abbreviated. See function metabias.
backtransf A logical indicating whether results for transformed rates (argument sm != "IR")
should be back transformed in printouts and plots. If TRUE (default), results will
be presented as incidence rates; otherwise transformed rates will be shown.
irscale A numeric defining a scaling factor for printing of rates.
irunit A character string specifying the time unit used to calculate rates, e.g. person-
years.
text.fixed A character string used in printouts and forest plot to label the pooled fixed effect
estimate.
metarate 179

text.random A character string used in printouts and forest plot to label the pooled random
effects estimate.
text.predict A character string used in printouts and forest plot to label the prediction inter-
val.
text.w.fixed A character string used to label weights of fixed effect model.
text.w.random A character string used to label weights of random effects model.
title Title of meta-analysis / systematic review.
complab Comparison label.
outclab Outcome label.
subgroup An optional vector to conduct a meta-analysis with subgroups.
subgroup.name A character string with a name for the subgroup variable.
print.subgroup.name
A logical indicating whether the name of the subgroup variable should be printed
in front of the group labels.
sep.subgroup A character string defining the separator between name of subgroup variable and
subgroup label.
test.subgroup A logical value indicating whether to print results of test for subgroup differ-
ences.
prediction.subgroup
A logical indicating whether prediction intervals should be printed for sub-
groups.
byvar Deprecated argument (replaced by ’subgroup’).
keepdata A logical indicating whether original data (set) should be kept in meta object.
warn A logical indicating whether the addition of incr to studies with zero events
should result in a warning.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
control An optional list to control the iterative process to estimate the between-study
variance τ 2 . This argument is passed on to rma.uni or rma.glmm, respectively.
... Additional arguments passed on to rma.glmm function.

Details
This function provides methods for fixed effect and random effects meta-analysis of single incidence
rates to calculate an overall rate. Note, you should use R function metainc to compare incidence
rates of pairwise comparisons instead of using metarate for each treatment arm separately which
will break randomisation in randomised controlled trials.
The following transformations of incidence rates are implemented to calculate an overall rate:

• Log transformation (sm = "IRLN", default)

• Square root transformation (sm = "IRS")
• Freeman-Tukey Double arcsine transformation (sm = "IRFT")
180 metarate

• No transformation (sm = "IR")

By default (argument method = "Inverse"), the inverse variance method (Borenstein et al., 2010) is
used for pooling by calling metagen internally. A random intercept Poisson regression model (Stij-
nen et al., 2010) can be utilised instead with argument method = "GLMM" which calls the rma.glmm
function from R package metafor.
Default settings are utilised for several arguments (assignments using gs function). These defaults
can be changed for the current R session using the settings.meta function.
Furthermore, R function update.meta can be used to rerun a meta-analysis with different settings.

Continuity correction:
If the summary measure (argument sm) is equal to "IR" or "IRLN", a continuity correction is
applied if any study has zero events, i.e., an incidence rate of 0.
By default, 0.5 is used as continuity correction (argument incr). This continuity correction is
used both to calculate individual study results with confidence limits and to conduct meta-analysis
based on the inverse variance method.
For the Freeman-Tukey (Freeman & Tukey, 1950) and square root transformation as well as
GLMMs no continuity correction is used.

Estimation of between-study variance:

Confidence interval for the between-study variance:

The following methods to calculate a confidence interval for τ 2 and τ are available.

Argument Method
method.tau.ci = "J" Method by Jackson
method.tau.ci = "BJ" Method by Biggerstaff and Jackson
method.tau.ci = "QP" Q-Profile method

Hartung-Knapp method:
metarate 181

Hartung and Knapp (2001a,b) proposed an alternative method for random effects meta-analysis
based on a refined variance estimator for the treatment estimate. Simulation studies (Hartung and
Knapp, 2001a,b; IntHout et al., 2014; Langan et al., 2019) show improved coverage probabilities
compared to the classic random effects method.
In rare settings with very homogeneous treatment estimates, the Hartung-Knapp variance estimate
can be arbitrarily small resulting in a very narrow confidence interval (Knapp and Hartung, 2003;
Wiksten et al., 2016). In such cases, an ad hoc variance correction has been proposed by utilising
the variance estimate from the classic random effects model with the HK method (Knapp and
Hartung, 2003; IQWiQ, 2020). An alternative approach is to use the wider confidence interval of
classic fixed or random effects meta-analysis and the HK method (Wiksten et al., 2016; Jackson
et al., 2017).
Argument adhoc.hakn can be used to choose the ad hoc method:

Argument Ad hoc method

For GLMMs, a method similar to Knapp and Hartung (2003) is implemented, see description of
argument tdist in rma.glmm, and the ad hoc variance correction is not available.

Specify the null hypothesis of test for an overall effect:

Argument null.effect can be used to specify the rate used under the null hypothesis in a test
for an overall effect.
By default (null.effect = NA), no hypothesis test is conducted as it is unclear which value is a
sensible choice for the data at hand. An overall rate of 2, for example, could be tested by setting
argument null.effect = 2.
Note, all tests for an overall effect are two-sided with the alternative hypothesis that the effect is
unequal to null.effect.
182 metarate

Exclusion of studies from meta-analysis:

Presentation of meta-analysis results:

Value
An object of class c("metarate","meta") with corresponding print, summary, and forest func-
tions. The object is a list containing the following components:
event, n, studlab, exclude,
As defined above.
sm, incr, allincr, addincr, method.ci,
As defined above.
level, level.ma,
As defined above.
fixed, random, As defined above.
overall, overall.hetstat,
As defined above.
hakn, adhoc.hakn, method.tau, method.tau.ci,
As defined above.
tau.preset, TE.tau, null.hypothesis,
As defined above.
method.bias, tau.common, title, complab, outclab,
As defined above.
subgroup, subgroup.name, print.subgroup.name, sep.subgroup, warn
As defined above.
TE, seTE Estimated (un)transformed incidence rate and its standard error for individual
studies.
lower, upper Lower and upper confidence interval limits for individual studies.
zval, pval z-value and p-value for test of treatment effect for individual studies.
w.fixed, w.random
Weight of individual studies (in fixed and random effects model).
metarate 183

TE.fixed, seTE.fixed
Estimated overall (un)transformed incidence rate and standard error (fixed effect
model).
lower.fixed, upper.fixed
Lower and upper confidence interval limits (fixed effect model).
statistic.fixed, pval.fixed
z-value and p-value for test of overall effect (fixed effect model).
TE.random, seTE.random
Estimated overall (un)transformed incidence rate and standard error (random
effects model).
lower.random, upper.random
Lower and upper confidence interval limits (random effects model).
statistic.random, pval.random
z-value or t-value and corresponding p-value for test of overall effect (random
effects model).
prediction, level.predict
As defined above.
seTE.predict Standard error utilised for prediction interval.
lower.predict, upper.predict
Lower and upper limits of prediction interval.
k Number of studies combined in meta-analysis.
Q Heterogeneity statistic Q.
df.Q Degrees of freedom for heterogeneity statistic.
pval.Q P-value of heterogeneity test.
Q.LRT Heterogeneity statistic for likelihood-ratio test (only if method = "GLMM").
df.Q.LRT Degrees of freedom for likelihood-ratio test
pval.Q.LRT P-value of likelihood-ratio test.
tau2 Between-study variance τ 2 .
se.tau2 Standard error of τ 2 .
lower.tau2, upper.tau2
Lower and upper limit of confidence interval for τ 2 .
tau Square-root of between-study variance τ .
lower.tau, upper.tau
Lower and upper limit of confidence interval for τ .
H Heterogeneity statistic H.
lower.H, upper.H
Lower and upper confidence limit for heterogeneity statistic H.
I2 Heterogeneity statistic I2 .
lower.I2, upper.I2
Lower and upper confidence limit for heterogeneity statistic I2 .
Rb Heterogeneity statistic Rb .
lower.Rb, upper.Rb
Lower and upper confidence limit for heterogeneity statistic Rb .
184 metarate

method A character string indicating method used for pooling: "Inverse"

df.hakn Degrees of freedom for test of treatment effect for Hartung-Knapp method (only
if hakn = TRUE).
bylevs Levels of grouping variable - if subgroup is not missing.
TE.fixed.w, seTE.fixed.w
Estimated treatment effect and standard error in subgroups (fixed effect model)
- if subgroup is not missing.
lower.fixed.w, upper.fixed.w
Lower and upper confidence interval limits in subgroups (fixed effect model) -
if subgroup is not missing.
statistic.fixed.w, pval.fixed.w
z-value and p-value for test of treatment effect in subgroups (fixed effect model)
- if subgroup is not missing.
TE.random.w, seTE.random.w
Estimated treatment effect and standard error in subgroups (random effects model)
- if subgroup is not missing.
lower.random.w, upper.random.w
Lower and upper confidence interval limits in subgroups (random effects model)
- if subgroup is not missing.
statistic.random.w, pval.random.w
z-value or t-value and corresponding p-value for test of treatment effect in sub-
groups (random effects model) - if subgroup is not missing.
w.fixed.w, w.random.w
Weight of subgroups (in fixed and random effects model) - if subgroup is not
missing.
df.hakn.w Degrees of freedom for test of treatment effect for Hartung-Knapp method in
subgroups - if subgroup is not missing and hakn = TRUE.
n.harmonic.mean.w
Harmonic mean of number of observations in subgroups (for back transfor-
mation of Freeman-Tukey Double arcsine transformation) - if subgroup is not
missing.
event.w Number of events in subgroups - if subgroup is not missing.
n.w Number of observations in subgroups - if subgroup is not missing.
k.w Number of studies combined within subgroups - if subgroup is not missing.
k.all.w Number of all studies in subgroups - if subgroup is not missing.
Q.w.fixed Overall within subgroups heterogeneity statistic Q (based on fixed effect model)
- if subgroup is not missing.
Q.w.random Overall within subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing (only calculated if argument tau.common is
TRUE).
df.Q.w Degrees of freedom for test of overall within subgroups heterogeneity - if subgroup
is not missing.
pval.Q.w.fixed P-value of within subgroups heterogeneity statistic Q (based on fixed effect
model) - if subgroup is not missing.
metarate 185

pval.Q.w.random
P-value of within subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
Q.b.fixed Overall between subgroups heterogeneity statistic Q (based on fixed effect model)
- if subgroup is not missing.
Q.b.random Overall between subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
df.Q.b Degrees of freedom for test of overall between subgroups heterogeneity - if
subgroup is not missing.
pval.Q.b.fixed P-value of between subgroups heterogeneity statistic Q (based on fixed effect
model) - if subgroup is not missing.
pval.Q.b.random
P-value of between subgroups heterogeneity statistic Q (based on random effects
model) - if subgroup is not missing.
tau.w Square-root of between-study variance within subgroups - if subgroup is not
missing.
H.w Heterogeneity statistic H within subgroups - if subgroup is not missing.
lower.H.w, upper.H.w
Lower and upper confidence limit for heterogeneity statistic H within subgroups
- if subgroup is not missing.
I2.w Heterogeneity statistic I2 within subgroups - if subgroup is not missing.
lower.I2.w, upper.I2.w
Lower and upper confidence limit for heterogeneity statistic I2 within subgroups
- if subgroup is not missing.
incr.event Increment added to number of events.
keepdata As defined above.
data Original data (set) used in function call (if keepdata = TRUE).
subset Information on subset of original data used in meta-analysis (if keepdata =
TRUE).
.glmm.fixed GLMM object generated by call of rma.glmm function (fixed effect model).
.glmm.random GLMM object generated by call of rma.glmm function (random effects model).
call Function call.
version Version of R package meta used to create object.
version.metafor
Version of R package metafor used for GLMMs.

Author(s)

Guido Schwarzer <[email protected]>

186 metarate

References
Borenstein M, Hedges LV, Higgins JP, Rothstein HR (2010): A basic introduction to fixed-effect
and random-effects models for meta-analysis. Research Synthesis Methods, 1, 97–111
Freeman MF & Tukey JW (1950): Transformations related to the angular and the square root.
Annals of Mathematical Statistics, 21, 607–11
Higgins JPT, Thompson SG, Spiegelhalter DJ (2009): A re-evaluation of random-effects meta-
analysis. Journal of the Royal Statistical Society: Series A, 172, 137–59
Hartung J, Knapp G (2001a): On tests of the overall treatment effect in meta-analysis with normally
distributed responses. Statistics in Medicine, 20, 1771–82
Hartung J, Knapp G (2001b): A refined method for the meta-analysis of controlled clinical trials
with binary outcome. Statistics in Medicine, 20, 3875–89
IntHout J, Ioannidis JPA, Borm GF (2014): The Hartung-Knapp-Sidik-Jonkman method for random
effects meta-analysis is straightforward and considerably outperforms the standard DerSimonian-
Laird method. BMC Medical Research Methodology, 14, 25
IQWiG (2020): General Methods: Version 6.0. https://www.iqwig.de/en/about-us/methods/
methods-paper/
Jackson D, Law M, Rücker G, Schwarzer G (2017): The Hartung-Knapp modification for random-
effects meta-analysis: A useful refinement but are there any residual concerns? Statistics in Medicine,
36, 3923–34
Langan D, Higgins JPT, Jackson D, Bowden J, Veroniki AA, Kontopantelis E, et al. (2019): A com-
parison of heterogeneity variance estimators in simulated random-effects meta-analyses. Research
Synthesis Methods, 10, 83–98
Stijnen T, Hamza TH, Ozdemir P (2010): Random effects meta-analysis of event outcome in the
framework of the generalized linear mixed model with applications in sparse data. Statistics in
Medicine, 29, 3046–67
Viechtbauer W (2010): Conducting Meta-Analyses in R with the Metafor Package. Journal of
Statistical Software, 36, 1–48
Wiksten A, Rücker G, Schwarzer G (2016): Hartung-Knapp method is not always conservative
compared with fixed-effect meta-analysis. Statistics in Medicine, 35, 2503–15

See Also
update.meta, metacont, metagen, print.meta

Examples
# Apply various meta-analysis methods to estimate incidence rates
#
m1 <- metarate(4:1, c(10, 20, 30, 40))
m2 <- update(m1, sm = "IR")
m3 <- update(m1, sm = "IRS")
m4 <- update(m1, sm = "IRFT")
#
m1
m2
m3
metareg 187

m4
#
forest(m1)
forest(m1, irscale = 100)
forest(m1, irscale = 100, irunit = "person-days")
forest(m1, backtransf = FALSE)
## Not run:
forest(m2)
forest(m3)
forest(m4)

## End(Not run)

m5 <- metarate(40:37, c(100, 200, 300, 400), sm = "IRFT")

metareg Meta-regression

Description
Meta-regression for objects of class meta. This is a wrapper function for the R function rma.uni in
the R package metafor (Viechtbauer 2010).

Usage
metareg(
x,
formula,
method.tau = x$method.tau,
hakn = x$hakn,
level.ma = x$level.ma,
intercept = TRUE,
...
)

Arguments
x An object of class meta.
formula Either a character string or a formula object.
method.tau A character string indicating which method is used to estimate the between-
study variance tau-squared. Either "FE", "DL", "REML", "ML", "HS", "SJ", "HE",
or "EB", can be abbreviated.
hakn A logical indicating whether the method by Hartung and Knapp should be used
to adjust test statistics and confidence intervals.
level.ma The level used to calculate confidence intervals for parameter estimates in the
meta-regression model.
188 metareg

intercept A logical indicating whether an intercept should be included in the meta-regression

model.
... Additional arguments passed to R function rma.uni.

Details

This R function is a wrapper function for R function rma.uni in the R package metafor (Viecht-
bauer 2010).
Note, results are not back-transformed in printouts of meta-analyses using summary measures with
transformations, e.g., log risk ratios are printed instead of the risk ratio if argument sm = "RR" and
logit transformed proportions are printed if argument sm = "PLOGIT".
Argument ’. . . ’ can be used to pass additional arguments to R function rma.uni. For example,
argument control to provide a list of control values for the iterative estimation algorithm. See help
page of R function rma.uni for more details.

Value

An object of class c("metareg","rma.uni","rma"). Please look at the help page of R function

rma.uni for more details on the output from this function.
In addition, a list .meta is added to the output containing the following components:

x, formula, method.tau, hakn, level.ma, intercept

As defined above.
dots Information provided in argument ’. . . ’.
call Function call.
version Version of R package meta used to create object.
version.metafor
Version of R package metafor used to create object.

Author(s)

Guido Schwarzer <[email protected]>

References

Viechtbauer W (2010): Conducting Meta-Analyses in R with the Metafor Package. Journal of

Statistical Software, 36, 1–48

See Also

bubble, summary.meta, metagen

metareg 189

Examples

data(Fleiss1993cont)
# Add some (fictitious) grouping variables:
Fleiss1993cont$age <- c(55, 65, 55, 65, 55)
Fleiss1993cont$region <- c("Europe", "Europe", "Asia", "Asia", "Europe")

m1 <- metacont(n.psyc, mean.psyc, sd.psyc, n.cont, mean.cont, sd.cont,

data = Fleiss1993cont, sm = "MD")
## Not run:
# Warnings due to wrong ordering of arguments (order has changed
# with version 3.0-0 of R package meta)
#
metareg(~ region, m1)
metareg(~ region, data = m1)

# Warning as no information on covariate is available

#
metareg(m1)

## End(Not run)

# Do meta-regression for covariate region

#
mu2 <- update(m1, subgroup = region, tau.common = TRUE, fixed = FALSE)
metareg(mu2)

# Same result for

# - tau-squared
# - test of heterogeneity
# - test for subgroup differences
# (as argument 'tau.common' was used to create mu2)
#
mu2
metareg(mu2, intercept = FALSE)
metareg(m1, region)

# Different result for

# - tau-squared
# - test of heterogeneity
# - test for subgroup differences
# (as argument 'tau.common' is - by default - FALSE)
#
mu1 <- update(m1, subgroup = region)
mu1

# Generate bubble plot

#
bubble(metareg(mu2))

# Do meta-regression with two covariates

#
metareg(mu1, region + age)
190 nnt

# Do same meta-regressions using formula notation

#
metareg(m1, ~ region)
metareg(mu1, ~ region + age)

# Do meta-regression using REML method and print intermediate

# results for iterative estimation algorithm; furthermore print
# results with three digits.
#
metareg(mu1, region, method.tau = "REML",
control = list(verbose = TRUE), digits = 3)

# Use Hartung-Knapp method

#
mu3 <- update(mu2, hakn = TRUE)
mu3
metareg(mu3, intercept = FALSE)

nnt Calculate the number needed to treat (NNT)

Description
Calculate the number needed to treat (NNT) from estimated risk difference, risk ratio, or odds ratio,
and a baseline risk.

Usage
nnt(x, ...)

## S3 method for class 'meta'

nnt(x, p.c, fixed = x$fixed, random = x$random, ...)

## Default S3 method:
nnt(x, p.c, sm, lower, upper, ...)

## S3 method for class 'nnt.meta'

print(
x,
fixed = x$fixed,
random = x$random,
digits = gs("digits"),
digits.prop = gs("digits.prop"),
big.mark = gs("big.mark"),
...
)
nnt 191

Arguments

x An object of class meta, or estimated treatment effect, i.e., risk difference(s),

risk ratio(s), or odds ratio(s).
... Additional arguments (ignored at the moment).
p.c Baseline risk (control group event probability).
fixed A logical indicating whether NNTs should be calculated based on fixed effect
estimate.
random A logical indicating whether NNTs should be calculated based on random ef-
fects estimate.
sm Summary measure.
lower Lower confidence interval limit.
upper Upper confidence interval limit.
digits Minimal number of significant digits, see print.default.
digits.prop Minimal number of significant digits for proportions, see print.default.
big.mark A character used as thousands separator.

Details

The number needed to treat (NNT) can be easily computed from an estimated risk difference (RD),
risk ratio (RR), or odds ratio (OR) and a given baseline risk (Higgins & Green, 2011, section 12.5).
Accordlingly, this function can be used to calculate NNTs for meta-analyses generated with metabin
or metagen if argument sm was equal to "RD", "RR", or "OR". It is also possible to directly provide
estimated treatment effects without conducting a meta-analysis (see Examples).
The baseline risk can be specified using argument p.c. If this argument is missing, the minimum,
mean, and maximum of the control event probabilities in the meta-analysis are used for metabin;
otherwise the control event probabilities 0.1, 0.2, . . . , 0.9 are used.

Author(s)

Guido Schwarzer <[email protected]>

References

Higgins, J.P.T and S. Green (2011): Cochrane Handbook for Systematic Reviews of Interventions
Version 5.1.0 [Updated March 2011]. The Cochrane Library: http://www.cochrane-handbook.org

See Also

metabin, metagen
192 Olkin1995

Examples
# Calculate NNT for RD = -0.21
# (Cochrane Handbook, version 5.1, subsection 12.5.4.1)
nnt(-0.21, sm = "RD")

# Calculate NNT for RR = 0.92 and baseline risk p.c = 0.3

# (Cochrane Handbook, version 5.1, subsection 12.5.4.2)
nnt(0.92, p.c = 0.3, sm = "RR")

# Calculate NNT for OR = 0.73 and baseline risk p.c = 0.3

# (Cochrane Handbook, version 5.1, subsection 12.5.4.3)
nnt(0.73, p.c = 0.3, sm = "OR")

# Use Mantel-Haenszel odds ratio to calculate NNTs

data(Olkin1995)
m1 <- metabin(ev.exp, n.exp, ev.cont, n.cont, data = Olkin1995,
random = FALSE)
nnt(m1, random = TRUE)

Olkin1995 Thrombolytic Therapy after Acute Myocardial Infarction

Description
Meta-analysis on Thrombolytic Therapy after Acute Myocardial Infarction

Format
A data frame with the following columns:

author first author

year year of publication
ev.exp number of events in experimental group
n.exp number of observations in experimental group
ev.cont number of events in control group
n.cont number of observations in control group

Source
Olkin I (1995): Statistical and theoretical considerations in meta-analysis. Journal of Clinical
Epidemiology, 48, 133–46

Examples
data(Olkin1995)
metabin(ev.exp, n.exp, ev.cont, n.cont, data = Olkin1995)
or2smd 193

or2smd Conversion from log odds ratio to standardised mean difference

Description
Conversion from log odds ratio to standardised mean difference using method by Hasselblad &
Hedges (1995) or Cox (1970).

Usage
or2smd(
lnOR,
selnOR,
studlab,
data = NULL,
subset = NULL,
exclude = NULL,
method = "HH",
...
)

Arguments
lnOR Log odds ratio(s) or meta-analysis object.
selnOR Standard error(s) of log odds ratio(s) (ignored if argument lnOR is a meta-
analysis object).
studlab An optional vector with study labels (ignored if argument lnOR is a meta-analysis
object).
data An optional data frame containing the study information (ignored if argument
lnOR is a meta-analysis object).
subset An optional vector specifying a subset of studies to be used (ignored if argument
lnOR is a meta-analysis object).
exclude An optional vector specifying studies to exclude from meta-analysis, however, to
include in printouts and forest plots (ignored if argument lnOR is a meta-analysis
object).
method A character string indicating which method is used to convert log odds ratios to
standardised mean differences. Either "HH" or "CS", can be abbreviated.
... Additional arguments passed on to metagen (ignored if argument lnOR is a
meta-analysis object).

Details
This function implements the following methods for the conversion from log odds ratios to stan-
dardised mean difference:
194 or2smd

• Hasselblad & Hedges (1995) assuming logistic distributions (method == "HH")

• Cox (1970) and Cox & Snell (1989) assuming normal distributions (method == "CS")

Internally, metagen is used to conduct a meta-analysis with the standardised mean difference as
summary measure.
Argument lnOR can be either a vector of log odds ratios or a meta-analysis object created with
metabin or metagen and the odds ratio as summary measure.
Argument selnOR is mandatory if argument lnOR is a vector and ignored otherwise. Additional
arguments in ... are only passed on to metagen if argument lnOR is a vector.

Value
An object of class "meta" and "metagen"; see metagen.

Author(s)
Guido Schwarzer <[email protected]>

References
Borenstein M, Hedges LV, Higgins JPT, Rothstein HR (2009): Introduction to Meta-Analysis.
Chichester: Wiley
Cox DR (1970): Analysis of Binary Data. London: Chapman and Hall / CRC
Cox DR, Snell EJ (1989): Analysis of Binary Data (2nd edition). London: Chapman and Hall /
CRC
Hasselblad V, Hedges LV (1995): Meta-analysis of screening and diagnostic tests. Psychological
Bulletin, 117, 167–78

See Also
smd2or, metabin, metagen, metacont

Examples
# Example from Borenstein et al. (2009), Chapter 7
#
mb <- or2smd(0.9069, sqrt(0.0676))
# TE = standardised mean difference (SMD); seTE = standard error of SMD
data.frame(SMD = round(mb$TE, 4), varSMD = round(mb$seTE^2, 4))

# Use dataset from Fleiss (1993)

#
data(Fleiss1993bin)
m1 <- metabin(d.asp, n.asp, d.plac, n.plac,
data = Fleiss1993bin, studlab = paste(study, year),
sm = "OR", random = FALSE)
or2smd(m1)
Pagliaro1992 195

Pagliaro1992 Meta-analysis on Prevention of First Bleeding in Cirrhosis

Description
Meta-analysis on Prevention of First Bleeding in Cirrhosis comparing beta-blocker or sclerotherapy
with placebo.

Format
A data frame with the following columns:

id study id
treat.exp treatment in experimental group
logOR log odds ratio
selogOR standard error of log odds ratio
bleed.exp number of bleedings in experimental group
n.cont number of observations in experimental group
bleed.plac number of bleedings in placebo group
n.plac number of observations in placebo group

Source

Pagliaro L, D’Amico G et al. (1992): Prevention of first bleeding in cirrhosis. Annals in Internal
Medicine, 117, 59–70

Examples

data(Pagliaro1992)
sclero <- subset(Pagliaro1992, treat.exp == "Sclerotherapy")

m <- metagen(logOR, selogOR, data = sclero, sm = "OR")

# Thompson & Sharp (1999), Table IV, method (2)

metabias(m, method = "Egger")

# Thompson & Sharp (1999), Table IV, method (3a)

metabias(m, method = "Thompson")

# Thompson & Sharp (1999), Table IV, method (3b)

update(m, method.tau = "ML")
metabias(update(m, method.tau = "ML"), method = "Thompson")
196 print.meta

print.meta Print meta-analysis results

Description
Print method for objects of class meta.
R function cilayout can be utilised to change the layout to print confidence intervals (both in printout
from print.meta and print.summary.meta function as well as in forest plots). The default layout is
"[lower; upper]". Another popular layout is "(lower - upper)" which is used throughout an R session
by using R command cilayout("("," -").
Argument pscale can be used to rescale single proportions or risk differences, e.g. pscale = 1000
means that proportions are expressed as events per 1000 observations. This is useful in situations
with (very) low event probabilities.
Argument irscale can be used to rescale single rates or rate differences, e.g. irscale = 1000
means that rates are expressed as events per 1000 time units, e.g. person-years. This is useful in
situations with (very) low rates. Argument irunit can be used to specify the time unit used in
individual studies (default: "person-years"). This information is printed in summaries and forest
plots if argument irscale is not equal to 1.

Usage
## S3 method for class 'meta'
print(
x,
fixed = x$fixed,
random = x$random,
prediction = x$prediction,
overall = x$overall,
overall.hetstat = x$overall.hetstat,
test.subgroup = x$test.subgroup,
test.subgroup.fixed = test.subgroup & fixed,
test.subgroup.random = test.subgroup & random,
prediction.subgroup = x$prediction.subgroup,
backtransf = x$backtransf,
pscale = x$pscale,
irscale = x$irscale,
irunit = x$irunit,
subgroup.name = x$subgroup.name,
print.subgroup.name = x$print.subgroup.name,
sep.subgroup = x$sep.subgroup,
nchar.subgroup = 35,
header = TRUE,
print.CMH = x$print.CMH,
digits = gs("digits"),
digits.stat = gs("digits.stat"),
digits.pval = max(gs("digits.pval"), 2),
print.meta 197

digits.pval.Q = max(gs("digits.pval.Q"), 2),

digits.Q = gs("digits.Q"),
digits.tau2 = gs("digits.tau2"),
digits.tau = gs("digits.tau"),
digits.H = gs("digits.H"),
digits.I2 = gs("digits.I2"),
scientific.pval = gs("scientific.pval"),
big.mark = gs("big.mark"),
zero.pval = gs("zero.pval"),
JAMA.pval = gs("JAMA.pval"),
print.tau2 = TRUE,
print.tau = TRUE,
print.I2 = gs("print.I2"),
print.H = gs("print.H"),
print.Rb = gs("print.Rb"),
text.tau2 = gs("text.tau2"),
text.tau = gs("text.tau"),
text.I2 = gs("text.I2"),
text.Rb = gs("text.Rb"),
details.methods = TRUE,
warn.backtransf = FALSE,
...
)

cilayout(
bracket = gs("CIbracket"),
separator = gs("CIseparator"),
lower.blank = gs("CIlower.blank"),
upper.blank = gs("CIupper.blank")
)

Arguments
x An object of class meta.
fixed A logical indicating whether results for fixed effect meta-analysis should be
printed.
random A logical indicating whether results for random effects meta-analysis should be
printed.
prediction A logical indicating whether a prediction interval should be printed.
overall A logical indicating whether overall summaries should be reported. This argu-
ment is useful in a meta-analysis with subgroups if overall results should not be
reported.
overall.hetstat
A logical value indicating whether to print heterogeneity measures for overall
treatment comparisons. This argument is useful in a meta-analysis with sub-
groups if heterogeneity statistics should only be printed on subgroup level.
test.subgroup A logical value indicating whether to print results of test for subgroup differ-
ences.
198 print.meta

test.subgroup.fixed
A logical value indicating whether to print results of test for subgroup differ-
ences (based on fixed effect / common effect model).
test.subgroup.random
A logical value indicating whether to print results of test for subgroup differ-
ences (based on random effects model).
prediction.subgroup
A logical indicating whether prediction intervals should be printed for sub-
groups.
backtransf A logical indicating whether printed results should be back transformed. If
backtransf=TRUE, results for sm="OR" are printed as odds ratios rather than
log odds ratios and results for sm="ZCOR" are printed as correlations rather than
Fisher’s z transformed correlations, for example.
pscale A numeric giving scaling factor for printing of single event probabilities or risk
differences, i.e. if argument sm is equal to "PLOGIT", "PLN", "PRAW", "PAS",
"PFT", or "RD".
irscale A numeric defining a scaling factor for printing of single incidence rates or in-
cidence rate differences, i.e. if argument sm is equal to "IR", "IRLN", "IRS",
"IRFT", or "IRD".
irunit A character specifying the time unit used to calculate rates, e.g. person-years.
subgroup.name A character string with a name for the grouping variable.
print.subgroup.name
A logical indicating whether the name of the grouping variable should be printed
in front of the group labels.
sep.subgroup A character string defining the separator between label and levels of grouping
variable.
nchar.subgroup A numeric specifying the number of characters to print from subgroup labels.
header A logical indicating whether information on title of meta-analysis, comparison
and outcome should be printed at the beginning of the printout.
print.CMH A logical indicating whether result of the Cochran-Mantel-Haenszel test for
overall effect should be printed.
digits Minimal number of significant digits, see print.default.
digits.stat Minimal number of significant digits for z- or t-value of test for overall effect,
see print.default.
digits.pval Minimal number of significant digits for p-value of overall treatment effect, see
print.default.
digits.pval.Q Minimal number of significant digits for p-value of heterogeneity test, see print.default.
digits.Q Minimal number of significant digits for heterogeneity statistic Q, see print.default.
digits.tau2 Minimal number of significant digits for between-study variance τ 2 , see print.default.
digits.tau Minimal number of significant digits for τ , the square root of the between-study
variance τ 2 .
digits.H Minimal number of significant digits for H statistic, see print.default.
digits.I2 Minimal number of significant digits for I-squared and Rb statistic, see print.default.
print.rm5 199

scientific.pval
A logical specifying whether p-values should be printed in scientific notation,
e.g., 1.2345e-01 instead of 0.12345.
big.mark A character used as thousands separator.
zero.pval A logical specifying whether p-values should be printed with a leading zero.
JAMA.pval A logical specifying whether p-values for test of overall effect should be printed
according to JAMA reporting standards.
print.tau2 A logical specifying whether between-study variance τ 2 should be printed.
print.tau A logical specifying whether τ , the square root of the between-study variance
τ 2 , should be printed.
print.I2 A logical specifying whether heterogeneity statistic I2 should be printed.
print.H A logical specifying whether heterogeneity statistic H should be printed.
print.Rb A logical specifying whether heterogeneity statistic Rb should be printed.
text.tau2 Text printed to identify between-study variance τ 2 .
text.tau Text printed to identify τ , the square root of the between-study variance τ 2 .
text.I2 Text printed to identify heterogeneity statistic I2 .
text.Rb Text printed to identify heterogeneity statistic Rb .
details.methods
A logical specifying whether details on statistical methods should be printed.
warn.backtransf
A logical indicating whether a warning should be printed if backtransformed
proportions and rates are below 0 and backtransformed proportions are above 1.
... Additional arguments (passed on to prmatrix).
bracket A character with bracket symbol to print lower confidence interval: "[", "(", "{",
"".
separator A character string with information on separator between lower and upper con-
fidence interval.
lower.blank A logical indicating whether blanks between left bracket and lower confidence
limit should be printed.
upper.blank A logical indicating whether blanks between separator and upper confidence
limit should be printed.

print.rm5 Cochrane review: summary of meta-analyses

Description
Calculate and print a summary of all meta-analyses in a Cochrane review.

Usage
## S3 method for class 'rm5'
print(x, comp.no, outcome.no, ...)
200 print.rm5

Arguments

x An object of class rm5.

comp.no Comparison number.
outcome.no Outcome number.
... Additional arguments (passed on to metacr).

Details

This function can be used to redo all or selected meta-analyses of a Cochrane Review.
Review Manager 5 (RevMan 5) is the current software used for preparing and maintaining Cochrane
Reviews (https://training.cochrane.org/online-learning/core-software-cochrane-reviews/
revman). In RevMan 5, subgroup analyses can be defined and data from a Cochrane review can be
imported to R using the function read.rm5.
The R function metacr is called internally.

Author(s)

Guido Schwarzer <[email protected]>

References

Higgins, J.P.T and S. Green (2011): Cochrane Handbook for Systematic Reviews of Interventions
Version 5.1.0 [Updated March 2011]. The Cochrane Library: http://www.cochrane-handbook.org

See Also

summary.meta, metacr, read.rm5, metabias.rm5

Examples
# Locate export data file "Fleiss1993_CR.csv"
# in sub-directory of package "meta"
#
filename <- system.file("extdata", "Fleiss1993_CR.csv", package = "meta")
Fleiss1993_CR <- read.rm5(filename)

# Print results for all meta-analysis

#
Fleiss1993_CR

# Print results only for second outcome of first comparison

#
print(Fleiss1993_CR, comp.no = 1, outcome.no = 2)
print.summary.meta 201

print.summary.meta Print detailed meta-analysis results

Description
Print method for objects of class summary.meta.

Usage
## S3 method for class 'summary.meta'
print(
x,
sortvar,
fixed = x$x$fixed,
random = x$x$random,
details = FALSE,
ma = TRUE,
overall = x$overall,
backtransf = x$backtransf,
pscale = x$pscale,
irscale = x$irscale,
irunit = x$irunit,
digits = gs("digits"),
digits.se = gs("digits.se"),
digits.pval = max(gs("digits.pval"), 2),
digits.tau2 = gs("digits.tau2"),
digits.tau = gs("digits.tau"),
digits.I2 = gs("digits.I2"),
digits.prop = gs("digits.prop"),
digits.weight = gs("digits.weight"),
scientific.pval = gs("scientific.pval"),
zero.pval = gs("zero.pval"),
JAMA.pval = gs("JAMA.pval"),
big.mark = gs("big.mark"),
text.tau2 = gs("text.tau2"),
text.tau = gs("text.tau"),
text.I2 = gs("text.I2"),
truncate,
text.truncate = "*** Output truncated ***",
details.methods = TRUE,
warn.backtransf = FALSE,
...
)

Arguments
x An object of class summary.meta
202 print.summary.meta

sortvar An optional vector used to sort the individual studies (must be of same length as
x$TE).
fixed A logical indicating whether a fixed effect meta-analysis should be conducted.
random A logical indicating whether a random effects meta-analysis should be con-
ducted.
details A logical indicating whether further details of individual studies should be printed.
ma A logical indicating whether the summary results of the meta-analysis should be
printed.
overall A logical indicating whether overall summaries should be reported. This argu-
ment is useful in a meta-analysis with subgroups if overall results should not be
reported.
backtransf A logical indicating whether printed results should be back transformed. If
backtransf = TRUE, results for sm = "OR" are printed as odds ratios rather than
log odds ratios and results for sm = "ZCOR" are printed as correlations rather than
Fisher’s z transformed correlations, for example.
pscale A numeric giving scaling factor for printing of single event probabilities or risk
differences, i.e. if argument sm is equal to "PLOGIT", "PLN", "PRAW", "PAS",
"PFT", or "RD".
irscale A numeric defining a scaling factor for printing of single incidence rates or in-
cidence rate differences, i.e. if argument sm is equal to "IR", "IRLN", "IRS",
"IRFT", or "IRD".
irunit A character specifying the time unit used to calculate rates, e.g. person-years.
digits Minimal number of significant digits, see print.default.
digits.se Minimal number of significant digits for standard deviations and standard errors,
see print.default.
digits.pval Minimal number of significant digits for p-value of test of treatment effect, see
print.default.
digits.tau2 Minimal number of significant digits for between-study variance, see print.default.
digits.tau Minimal number of significant digits for square root of between-study variance,
see print.default.
digits.I2 Minimal number of significant digits for I-squared and Rb statistic, see print.default.
digits.prop Minimal number of significant digits for proportions, see print.default.
digits.weight Minimal number of significant digits for weights, see print.default.
scientific.pval
A logical specifying whether p-values should be printed in scientific notation,
e.g., 1.2345e-01 instead of 0.12345.
zero.pval A logical specifying whether p-values should be printed with a leading zero.
JAMA.pval A logical specifying whether p-values for test of overall effect should be printed
according to JAMA reporting standards.
big.mark A character used as thousands separator.
text.tau2 Text printed to identify between-study variance τ 2 .
print.summary.meta 203

text.tau Text printed to identify τ , the square root of the between-study variance τ 2 .
text.I2 Text printed to identify heterogeneity statistic I2 .
truncate An optional vector used to truncate the printout of results for individual studies
(must be a logical vector of same length as x$TE or contain numerical values).
text.truncate A character string printed if study results were truncated from the printout.
details.methods
A logical specifying whether details on statistical methods should be printed.
warn.backtransf
A logical indicating whether a warning should be printed if backtransformed
proportions and rates are below 0 and backtransformed proportions are above 1.
... Additional arguments (passed on to print.meta called internally).

Details
Print method for objects of class summary.meta giving detailed information on the meta-analysis.
Argument pscale can be used to rescale single proportions or risk differences, e.g. pscale = 1000
means that proportions are expressed as events per 1000 observations. This is useful in situations
with (very) low event probabilities.
Argument irscale can be used to rescale single rates or rate differences, e.g. irscale = 1000
means that rates are expressed as events per 1000 time units, e.g. person-years. This is useful in
situations with (very) low rates. Argument irunit can be used to specify the time unit used in
individual studies (default: "person-years"). This information is printed in summaries and forest
plots if argument irscale is not equal to 1.

Author(s)
Guido Schwarzer <[email protected]>

References
Cooper H & Hedges LV (1994), The Handbook of Research Synthesis. Newbury Park, CA: Russell
Sage Foundation.
Crippa A, Khudyakov P, Wang M, Orsini N, Spiegelman D (2016), A new measure of between-
studies heterogeneity in meta-analysis. Statistics in Medicine, 35, 3661–75.
Higgins JPT & Thompson SG (2002), Quantifying heterogeneity in a meta-analysis. Statistics in
Medicine, 21, 1539–58.

See Also
summary.meta, update.meta, metabin, metacont, metagen

Examples
data(Fleiss1993cont)
m1 <- metacont(n.psyc, mean.psyc, sd.psyc, n.cont, mean.cont, sd.cont,
data = Fleiss1993cont, sm = "SMD", studlab = paste(study, year))
sm1 <- summary(m1)
204 radial.meta

sm1

print(sm1, digits = 2)

## Not run:
# Use unicode characters to print tau^2, tau, and I^2
print(sm1,
text.tau2 = "\u03c4\u00b2",
text.tau = "\u03c4", text.I2 = "I\u00b2")

## End(Not run)

radial.meta Radial plot

Description
Draw a radial plot (also called Galbraith plot) which can be used to assess bias in meta-analysis.

Usage
## S3 method for class 'meta'
radial(
x,
xlim = NULL,
ylim = NULL,
xlab = "Inverse of standard error",
ylab = "Standardised treatment effect (z-score)",
fixed = TRUE,
axes = TRUE,
pch = 1,
text = NULL,
cex = 1,
col = NULL,
level = NULL,
...
)

## Default S3 method:
radial(
x,
y,
xlim = NULL,
ylim = NULL,
xlab = "Inverse of standard error",
ylab = "Standardised treatment effect (z-score)",
fixed = TRUE,
radial.meta 205

axes = TRUE,
pch = 1,
text = NULL,
cex = 1,
col = NULL,
level = NULL,
...
)

Arguments
x An object of class meta, or estimated treatment effect in individual studies.
xlim The x limits (min, max) of the plot.
ylim The y limits (min, max) of the plot.
xlab A label for the x-axis.
ylab A label for the y-axis.
fixed A logical indicating whether the pooled fixed effect estimate should be plotted.
axes A logical indicating whether axes should be drawn on the plot.
pch The plotting symbol used for individual studies.
text A character vector specifying the text to be used instead of plotting symbol.
cex The magnification to be used for plotting symbol.
col A vector with colour of plotting symbols.
level The confidence level utilised in the plot.
... Graphical arguments as in par may also be passed as arguments.
y Standard error of estimated treatment effect.

Details
A radial plot (Galbraith 1988a,b), also called Galbraith plot, is drawn in the active graphics window.
If fixed is TRUE, the pooled estimate of the fixed effect model is plotted. If level is not NULL,
the corresponding confidence limits are drawn.

Author(s)
Guido Schwarzer <[email protected]>

References
Galbraith RF (1988a): Graphical display of estimates having differing standard errors. Technomet-
rics, 30, 271–81
Galbraith RF (1988b): A note on graphical presentation of estimated odds ratios from several clin-
ical trials. Statistics in Medicine, 7, 889–94

See Also
metabias, metabin, metagen, funnel
206 read.mtv

Examples
data(Olkin1995)
m1 <- metabin(ev.exp, n.exp, ev.cont, n.cont,
data = Olkin1995, subset = c(41, 47, 51, 59),
studlab = paste(author, year), sm = "RR", method = "I")

# Radial plot
#
radial(m1, level = 0.95)

read.mtv Import RevMan 4 data files (.mtv)

Description
Reads a file created with RevMan 4 and creates a data frame from it.

Usage
read.mtv(file)

Arguments
file The name of a file to read data values from.

Details
Reads a file created with RevMan 4 (Menu: "File" - "Export" - "Analysis data file...") and creates a
data frame from it.

Value
A data frame containing the following components:

comp.no Comparison number.

outcome.no Outcome number.
group.no Group number.
studlab Study label.
year Year of publication.
event.e Number of events in experimental group.
n.e Number of observations in experimental group.
event.c Number of events in control group.
n.c Number of observations in control group.
mean.e Estimated mean in experimental group.
read.mtv 207

sd.e Standard deviation in experimental group.

mean.c Estimated mean in control group.
sd.c Standard deviation in control group.
O.E Observed minus expected (IPD analysis).
V Variance of O.E (IPD analysis).
order Ordering of studies.
conceal Concealment of treatment allocation.
grplab Group label.
type Type of outcome. D = dichotomous, C = continuous, P = IPD.
outclab Outcome label.
graph.exp Graph label for experimental group.
graph.cont Graph label for control group.
label.exp Label for experimental group.
label.cont Label for control group.
complab Comparison label.

Author(s)
Guido Schwarzer <[email protected]>

References
Review Manager (RevMan) [Computer program]. Version 4.2. Copenhagen: The Nordic Cochrane
Centre, The Cochrane Collaboration, 2003

# Same result as R Command example(Fleiss1993bin):

#
metabin(event.e, n.e, event.c, n.c,
data = fleiss1933.cc, subset = type == "D",
studlab = paste(studlab, year))

# Same result: example(Fleiss1993cont)

#
metacont(n.e, mean.e, sd.e, n.c, mean.c, sd.c,
208 read.rm5

data = fleiss1933.cc, subset = type == "C",

studlab = paste(studlab, year))

read.rm5 Import RevMan 5 analysis data

Description
Reads analysis data from Cochrane intervention review created with RevMan 5 and creates a data
frame from it.

Usage
read.rm5(
file,
sep = ",",
quote = "\"",
title,
numbers.in.labels = TRUE,
debug = 0
)

Arguments
file The name of a file to read data values from.
sep The field separator character (only considered for CSV-files). Values on each
line of the file are separated by this character. The comma is the default field
separator character in RevMan 5.
quote The set of quoting characters (only considered for CSV-files). In RevMan 5 a
"\"" is the default quoting character.
title Title of Cochrane review.
numbers.in.labels
A logical indicating whether comparision number and outcome number should
be printed at the beginning of the comparison (argument complab) and outcome
label (argument outclab); this is the default in RevMan 5.
debug An integer between 0 and 3 indicating whether to print debug messages (only
considered for RM5-files).

Details
Review Manager 5 (RevMan 5) was the software used for preparing and maintaining Cochrane re-
views (https://training.cochrane.org/online-learning/core-software-cochrane-reviews/
revman). RevMan 5 includes the ability to write systematic reviews of interventions, diagnostic test
accuracy reviews, methodology reviews and overviews of reviews.
read.rm5 209

This function provides the ability to read the analysis data from a Cochrane intervention review
created with RevMan 5; a data frame is created from it. Cochrane intervention reviews are based
on comparisons of two interventions.
By default in RevMan 5, the name of the exported CSV data file is the title of the Cochrane review.
Furthermore, the title is part of the RM5-file. Argument title can be used to overwrite the title of
the Cochrane review.

Import RM5-file:
A RM5-file (which is in a specific XML format) can be used directly to import the analysis dataset.
If the import fails, use argument debug = 3 for more details.

Import CSV-file:
In the past, the following (rather complicated) procedure based on a CSV-file generated within
RevMan 5 was necessary - which is only described here for backward compatibility.
In order to generate a data analysis file in RevMan 5 use the following Menu points: "File" -
"Export" - "Data and analyses". It is mandatory to include the following fields in the exported
data file by selecting them with the mouse cursor in the Export Analysis Data Wizard: (i) Compar-
ison Number, (ii) Outcome Number, (iii) Subgroup Number. When these fields are not selected
a corresponding error message will be printed in R. It is recommended to include all fields in the
exported data file except for the last field "Risk of bias tables". For example, in order to redo
the meta-analysis in R for the RevMan 5 data type "O-E and Variance" the fields "O-E" and
"Variance" have to be selected in the Export Analysis Data Wizard. If the last field "Risk of bias
tables" is selected the import in R fails with an error message "line X did not have Y elements".

Value
A data frame containing the following components:
comp.no Comparison number.
outcome.no Outcome number.
group.no Group number.
studlab Study label.
year Year of publication.
event.e Number of events in experimental group.
n.e Number of observations in experimental group.
event.c Number of events in control group.
n.c Number of observations in control group.
mean.e Estimated mean in experimental group.
sd.e Standard deviation in experimental group.
mean.c Estimated mean in control group.
sd.c Standard deviation in control group.
O.E Observed minus expected (IPD analysis).
V Variance of O.E (IPD analysis).
TE, seTE Estimated treatment effect and standard error of individual studies.
210 read.rm5

lower, upper Lower and upper limit of 95% confidence interval for treatment effect in indi-
vidual studies.
weight Weight of individual studies (according to meta-analytical method used in re-
spective meta-analysis - see details).
order Ordering of studies.
grplab Group label.
type Type of outcome. D = dichotomous, C = continuous, P = IPD.
method A character string indicating which method has been used for pooling of studies.
One of "Inverse", "MH", or "Peto".
sm A character string indicating which summary measure has been used for pooling
of studies.
model A character string indicating which meta-analytical model has been used (either
"Fixed" or "Random").
fixed A logical indicating whether fixed effect meta-analysis has been used in respec-
tive meta-analysis (see details).
random A logical indicating whether random effects meta-analysis has been used in re-
spective meta-analysis (see details).
outclab Outcome label.
k Total number of studies combined in respective meta-analysis).
event.e.pooled Number of events in experimental group in respective meta-analysis (see de-
tails).
n.e.pooled Number of observations in experimental group in respective meta-analysis (see
details).
event.c.pooled Number of events in control group in respective meta-analysis (see details).
n.c.pooled Number of observations in control group in respective meta-analysis (see de-
tails).
TE.pooled Estimated treatment effect in respective meta-analysis (see details).
lower, upper Lower and upper limit of 95% confidence interval for treatment effect in respec-
tive meta-analysis (see details).
weight.pooled Total weight in respective meta-analysis (see details).
Z.pooled Z-score for test of overall treatment effect in respective meta-analysis (see de-
tails).
pval.pooled P-value for test of overall treatment effect in respective meta-analysis (see de-
tails).
Q Heterogeneity statistic Q in respective meta-analysis (see details).
pval.Q P-value of heterogeneity statistic Q in respective meta-analysis (see details).
I2 Heterogeneity statistic I2 in respective meta-analysis (see details).
tau2 Between-study variance (moment estimator of DerSimonian-Laird) in respec-
tive meta-analysis.
Q.w Heterogeneity statistic Q within groups in respective meta-analysis (see details).
settings.meta 211

pval.Q.w P-value of heterogeneity statistic Q within groups in respective meta-analysis

(see details).
I2.w Heterogeneity statistic I2 within groups in respective meta-analysis (see details).
label.e Label for experimental group.
label.c Label for control group.
label.left Graph label on left side of forest plot.
label.right Graph label on right side of forest plot.
complab Comparison label.

Author(s)
Guido Schwarzer <[email protected]>

References
Review Manager (RevMan) [Computer program]. Version 5.4. The Cochrane Collaboration, 2020

See Also
summary.rm5, metabias.rm5, metabin, metacont, metagen, metacr, print.rm5

# Same result as R command example(Fleiss1993bin):

#
metacr(Fleiss1993_CR)

# Same result as R command example(Fleiss1993cont):

#
metacr(Fleiss1993_CR, 1, 2)

settings.meta Print and change default settings to conduct and print or plot meta-
analyses in R package meta.

Description
Print and change default settings to conduct and print or plot meta-analyses in R package meta.
The following general settings are available: Review Manager 5, Journal of the American Medical
Association.
212 settings.meta

Usage
settings.meta(..., quietly = TRUE)

Arguments
... Arguments to change default settings.
quietly A logical indicating whether information on settings should be printed.

Details
This function can be used to define defaults for several arguments (i.e., assignments using gs) of
the following R functions: metabin, metacont, metacor, metacr, metagen, metainc, metaprop,
metarate
Furthermore, some of these settings are considered to print meta-analysis results and to produce
forest plots.
The function can be used to either change individual settings (see Examples) or use one of the
following general settings:
• settings.meta("revman5")
• settings.meta("jama")
• settings.meta("iqwig5")
• settings.meta("iqwig6")
• settings.meta("geneexpr")
• settings.meta("meta4")
The first command can be used to reproduce meta-analyses from Cochrane reviews conducted with
Review Manager 5 (RevMan 5, https://training.cochrane.org/online-learning/core-software-cochrane-revie
revman) and specifies to use a RevMan 5 layout in forest plots.
The second command can be used to generate forest plots following instructions for authors of
the Journal of the American Medical Association (https://jamanetwork.com/journals/jama/
pages/instructions-for-authors/).Study labels according to JAMA guidelines can be gener-
ated using labels.meta.
The next commands implement the recommendations of the Institute for Quality and Efficiency in
Health Care, Germany (IQWiG) accordinging to General Methods 5 and 6, respectively (https:
//www.iqwig.de/en/about-us/methods/methods-paper/).
The setting "geneexpr" can be used to print p-values in scientific notation and to suppress the
calculation of confidence intervals for the between-study variance.
The last setting uses the default settings of R package meta, version 4 or below.
RevMan 5 settings, in detail:

Argument Value Comment

hakn FALSE method not available in RevMan 5
method.tau "DL" only available method in RevMan 5
tau.common FALSE common between-study variance in subgroups
MH.exact FALSE exact Mantel-Haenszel method
settings.meta 213

RR.Cochrane TRUE calculation of risk ratios

Q.Cochrane TRUE calculation of heterogeneity statistic
layout "RevMan5" layout for forest plots
test.overall TRUE print information on test of overall effect
digits.I2 0 number of digits for I-squared measure
digits.tau2 2 number of digits for tau-squared
digits.tau 4 number of digits for square root of tau-squared
CIbracket, "["
CIseparator ", " print confidence intervals as "[., .]"

JAMA settings:

Argument Value Comment

layout "JAMA" layout for forest plots
test.overall TRUE print information on test of overall effect
digits.I2 0 number of digits for I-squared measure
CIbracket, "("
CIseparator "-" print confidence intervals as "(.-.)"
zero.pval, TRUE print p-values with leading zero
JAMA.pval, TRUE round p-values to three digits (for 0.001 < p ≤ 0.01) or two digits (p > 0.01)

IQWiG, General Methods 5 settings:

Argument Value Comment

hakn TRUE Hartung-Knapp method
prediction TRUE Prediction interval

IQWiG, General Methods 6 settings:

Argument Value Comment

hakn TRUE Hartung-Knapp method
adhoc.hakn "ci" ad hoc variance correction
method.tau "PM" Paule-Mandel estimator for between-study variance
prediction TRUE Prediction interval

Settings for gene expression data:

Argument Value Comment

scientific.pval TRUE Scientific notation for p-values
method.tau.ci FALSE no confidence interval for
between-study heterogeneity variance

Settings for meta, version 4 or below:

214 settings.meta

Argument Value Comment

method.tau "DL" DerSimonian-Laird estimator

A list of all arguments with current settings is printed using the command settings.meta("print").
In order to reset all settings of R package meta the command settings.meta("reset") or settings.meta(reset
= TRUE) can be used.

Author(s)
Guido Schwarzer <[email protected]>

See Also
gs, forest.meta, print.meta, labels.meta

Examples
# Get listing of current settings
#
settings.meta()

# Meta-analyses using default settings

#
metabin(10, 20, 15, 20)
metaprop(4, 20)
metabin(10, 20, 15, 20, sm = "RD")
metaprop(4, 20, sm = "PLN")

# Change summary measure for R functions metabin and metaprop

# and store old settings
#
oldset <- settings.meta(smbin = "RD", smprop = "PLN")
#
metabin(10, 20, 15, 20)
metaprop(4, 20)

# Use old settings

#
settings.meta(oldset)

# Change level used to calculate confidence intervals

# (99%-CI for studies, 99.9%-CI for pooled effects)
#
metagen(1:3, 2:4 / 10, sm = "MD")
settings.meta(level = 0.99, level.ma = 0.999)
metagen(1:3, 2:4 / 10, sm = "MD")

# Always print a prediction interval

#
settings.meta(prediction = TRUE)
smd2or 215

metagen(1:3, 2:4 / 10, sm = "MD")

metagen(4:6, 4:2 / 10, sm = "MD")

# Try to set unknown argument results in a warning

#
try(settings.meta(unknownarg = TRUE))

# Reset to default settings of R package meta

#
settings.meta("reset")
metabin(10, 20, 15, 20)
metaprop(4, 20)
metagen(1:3, 2:4 / 10, sm = "MD")

# Do not back transform results (e.g. print log odds ratios instead
# of odds ratios, print transformed correlations / proportions
# instead of correlations / proportions)
#
settings.meta(backtransf = FALSE)
metabin(10, 20, 15, 20)
metaprop(4, 20)
metacor(c(0.85, 0.7, 0.95), c(20, 40, 10))

# Forest plot using RevMan 5 style

#
settings.meta("revman5")
forest(metagen(1:3, 2:4 / 10, sm = "MD", fixed = FALSE),
label.left = "Favours A", label.right = "Favours B",
colgap.studlab = "2cm", colgap.forest.left = "0.2cm")

# Forest plot using JAMA style

#
settings.meta("jama")
forest(metagen(1:3, 2:4 / 10, sm = "MD", fixed = FALSE),
label.left = "Favours A", label.right = "Favours B",
colgap.studlab = "2cm", colgap.forest.left = "0.2cm")

# Use slightly different layout for confidence intervals

# (especially useful if upper confidence limit can be negative)
#
settings.meta(CIseparator = " - ")
forest(metagen(-(1:3), 2:4 / 10, sm="MD", fixed=FALSE),
label.left="Favours A", label.right="Favours B",
colgap.studlab = "2cm", colgap.forest.left = "0.2cm")

# Use old settings

#
settings.meta(oldset)

smd2or Conversion from standardised mean difference to log odds ratio

216 smd2or

Description
Conversion from standardised mean difference to log odds ratio using method by Hasselblad &
Hedges (1995) or Cox (1970).

Usage
smd2or(
smd,
se.smd,
studlab,
data = NULL,
subset = NULL,
exclude = NULL,
method = "HH",
backtransf = gs("backtransf"),
...
)

Arguments
smd Standardised mean difference(s) (SMD) or meta-analysis object.
se.smd Standard error(s) of SMD (ignored if argument smd is a meta-analysis object).
studlab An optional vector with study labels (ignored if argument smd is a meta-analysis
object).
data An optional data frame containing the study information (ignored if argument
smd is a meta-analysis object).
subset An optional vector specifying a subset of studies to be used (ignored if argument
smd is a meta-analysis object).
exclude An optional vector specifying studies to exclude from meta-analysis, however, to
include in printouts and forest plots (ignored if argument smd is a meta-analysis
object).
method A character string indicating which method is used to convert SMDs to log odds
ratios. Either "HH" or "CS", can be abbreviated.
backtransf A logical indicating whether odds ratios (if TRUE) or log odds ratios (if FALSE)
should be shown in printouts and plots.
... Additional arguments passed on to metagen (ignored if argument smd is a meta-
analysis object).

Details
This function implements the following methods for the conversion from standardised mean differ-
ence to log odds ratio:

• Hasselblad & Hedges (1995) assuming logistic distributions (method == "HH")

• Cox (1970) and Cox & Snell (1989) assuming normal distributions (method == "CS")
smd2or 217

Internally, metagen is used to conduct a meta-analysis with the odds ratio as summary measure.
Argument smd can be either a vector of standardised mean differences or a meta-analysis object
created with metacont or metagen and the standardised mean difference as summary measure.
Argument se.smd is mandatory if argument smd is a vector and ignored otherwise. Additional
arguments in ... are only passed on to metagen if argument smd is a vector.

Value

An object of class "meta" and "metagen"; see metagen.

Author(s)

Guido Schwarzer <[email protected]>

References

Borenstein M, Hedges LV, Higgins JPT, Rothstein HR (2009): Introduction to Meta-Analysis.

Chichester: Wiley
Cox DR (1970): Analysis of Binary Data. London: Chapman and Hall / CRC
Cox DR, Snell EJ (1989): Analysis of Binary Data (2nd edition). London: Chapman and Hall /
CRC
Hasselblad V, Hedges LV (1995): Meta-analysis of screening and diagnostic tests. Psychological
Bulletin, 117, 167–78

See Also

or2smd, metacont, metagen, metabin

Examples
# Example from Borenstein et al. (2009), Chapter 7
#
mb <- smd2or(0.5, sqrt(0.0205), backtransf = FALSE)
# TE = log odds ratio; seTE = standard error of log odds ratio
data.frame(lnOR = round(mb$TE, 4), varlnOR = round(mb$seTE^2, 4))

# Use dataset from Fleiss (1993)

#
data(Fleiss1993cont)
m1 <- metacont(n.psyc, mean.psyc, sd.psyc, n.cont, mean.cont, sd.cont,
data = Fleiss1993cont, sm = "SMD",
studlab = paste(study, year))
smd2or(m1)
218 smoking

smoking Smoking example

Description
Meta-analyses on the effect of smoking on mortality risk.

Format
A data frame with the following columns:

study study label

participants total number of participants
d.smokers number of deaths in smokers’ group
py.smokers person years at risk in smokers’ group
d.nonsmokers number of deaths in non-smokers’ group
py.nonsmokers person years at risk in non-smokers’ group

Details
Data have been reconstructed based on the famous Smoking and Health Report to the Surgeon
General (Bayne-Jones S et al., 1964). Data sets can be used to evaluate the risk of smoking on
overall mortality (dataset smoking) and lung-cancer deaths (dataset lungcancer), respectively.
The person time is attributed such that the rate ratios are equal to the reported mortality ratios
implicitly assuming that the data have arisen from a homogeneous age group; more detailed infor-
mation by age is not available from the report. Note, the group of "non-smokers" actually consists
of all participants except those who are smokers of cigarettes only. Information on real non-smokers
is not available from the published Smoking and Health Report.

Source
Bayne-Jones S et al. (1964): Smoking and Health: Report of the Advisory Committee to the
Surgeon General of the United States. U-23 Department of Health, Education, and Welfare. Public
Health Service Publication No. 1103.

m1 <- metainc(d.smokers, py.smokers, d.nonsmokers, py.nonsmokers,

data = smoking, studlab = study)
print(m1, digits = 2)

data(lungcancer)
summary.meta 219

m2 <- metainc(d.smokers, py.smokers, d.nonsmokers, py.nonsmokers,

data = lungcancer, studlab = study)
print(m2, digits = 2)

summary.meta Summary of meta-analysis results

Description
Summary method for objects of class meta.

Usage
## S3 method for class 'meta'
summary(object, ...)

Arguments
object An object of class meta.
... Additional arguments (ignored).

Details
Review Manager 5 (RevMan 5) is the current software used for preparing and maintaining Cochrane
Reviews (https://training.cochrane.org/online-learning/core-software-cochrane-reviews/
revman). In RevMan 5, subgroup analyses can be defined and data from a Cochrane review can be
imported to Rusing the function read.rm5. If a meta-analysis is then conducted using function
metacr, information on subgroups is available in R (components subgroup, subgroup.name, and
print.subgroup.name, subgroup in an object of class "meta"). Accordingly, by using function
metacr there is no need to define subgroups in order to redo the statistical analysis conducted in the
Cochrane review.
Note, for an object of type metaprop, starting with version 3.7-0 of meta, list elements TE, lower
and upper in element study correspond to transformed proportions and confidence limits (regard-
less whether exact confidence limits are calculated; argument ciexact=TRUE in metaprop func-
tion). Accordingly, the following results are based on the same transformation defined by argument
sm: list elements TE, lower and upper in elements study, fixed, random, within.fixed and
within.random.
R function cilayout can be utilised to change the layout to print confidence intervals (both in printout
from print.meta and print.summary.meta function as well as in forest plots). The default layout is
"[lower; upper]". Another popular layout is "(lower - upper)" which is used throughout an R session
by using R command cilayout("("," -").
Argument pscale can be used to rescale single proportions or risk differences, e.g. pscale=1000
means that proportions are expressed as events per 1000 observations. This is useful in situations
with (very) low event probabilities.
220 summary.meta

Argument irscale can be used to rescale single rates or rate differences, e.g. irscale=1000
means that rates are expressed as events per 1000 time units, e.g. person-years. This is useful in
situations with (very) low rates. Argument irunit can be used to specify the time unit used in
individual studies (default: "person-years"). This information is printed in summaries and forest
plots if argument irscale is not equal to 1.

Value

An object of classes summary.meta and meta.

Author(s)

Guido Schwarzer <[email protected]>

References

Cooper H & Hedges LV (1994): The Handbook of Research Synthesis. Newbury Park, CA: Russell
Sage Foundation
Crippa A, Khudyakov P, Wang M, Orsini N, Spiegelman D (2016): A new measure of between-
studies heterogeneity in meta-analysis. Statistics in Medicine, 35, 3661–75
Higgins JPT & Thompson SG (2002): Quantifying heterogeneity in a meta-analysis. Statistics in
Medicine, 21, 1539–58

See Also

print.summary.meta, metabin, metacont, metagen

Examples
data(Fleiss1993cont)
m1 <- metacont(n.psyc, mean.psyc, sd.psyc, n.cont, mean.cont, sd.cont,
data = Fleiss1993cont, studlab = paste(study, year), sm = "SMD")
summary(m1)

summary(update(m1, subgroup = c(1, 2, 1, 1, 2), subgroup.name = "group"))

forest(update(m1, subgroup = c(1, 2, 1, 1, 2), subgroup.name = "group"))

## Not run:
# Use unicode characters to print tau^2, tau, and I^2
print(summary(m1),
text.tau2 = "\u03c4\u00b2", text.tau = "\u03c4", text.I2 = "I\u00b2")

## End(Not run)
summary.rm5 221

summary.rm5 Cochrane review: detailed summary of meta-analyses

Description
Calculate and print a detailed summary of all meta-analyses in a Cochrane review.

Usage
## S3 method for class 'rm5'
summary(object, comp.no, outcome.no, ...)

## S3 method for class 'summary.rm5'

print(x, ...)

Arguments
object An object of class rm5.
comp.no Comparison number.
outcome.no Outcome number.
... Additional arguments (passed on to metacr).
x An object of class summary.rm5.

Details
This function can be used to redo all or selected meta-analyses of a Cochrane Review.
Review Manager 5 (RevMan 5) is the current software used for preparing and maintaining Cochrane
Reviews (https://training.cochrane.org/online-learning/core-software-cochrane-reviews/
revman). In RevMan 5, subgroup analyses can be defined and data from a Cochrane review can be
imported to R using the function read.rm5.
The R function metacr is called internally.

Author(s)
Guido Schwarzer <[email protected]>

References
Higgins, J.P.T and S. Green (2011): Cochrane Handbook for Systematic Reviews of Interventions
Version 5.1.0 [Updated March 2011]. The Cochrane Library: http://www.cochrane-handbook.org

See Also
summary.meta, metacr, read.rm5, metabias.rm5
222 trimfill.meta

# Print summary results for all meta-analysis

#
summary(Fleiss1993_CR)

# Print summary results only for second outcome of first comparison

#
summary(Fleiss1993_CR, comp.no = 1, outcome.no = 2)

trimfill.meta Trim-and-fill method to adjust for bias in meta-analysis

Description
Trim-and-fill method for estimating and adjusting for the number and outcomes of missing studies
in a meta-analysis.

Usage
## S3 method for class 'meta'
trimfill(
x,
left = NULL,
ma.fixed = TRUE,
type = "L",
n.iter.max = 50,
level = x$level,
level.ma = x$level.ma,
fixed = FALSE,
random = TRUE,
hakn = x$hakn,
method.tau = x$method.tau,
method.tau.ci = x$method.tau.ci,
prediction = x$prediction,
level.predict = x$level.predict,
backtransf = x$backtransf,
pscale = x$pscale,
irscale = x$irscale,
irunit = x$irunit,
silent = TRUE,
...
trimfill.meta 223

## Default S3 method:
trimfill(
x,
seTE,
left = NULL,
ma.fixed = TRUE,
type = "L",
n.iter.max = 50,
sm = "",
studlab = NULL,
level = 0.95,
level.ma = level,
fixed = FALSE,
random = TRUE,
hakn = FALSE,
method.tau = "DL",
method.tau.ci = if (method.tau == "DL") "J" else "QP",
prediction = FALSE,
level.predict = level,
backtransf = TRUE,
pscale = 1,
irscale = 1,
irunit = "person-years",
silent = TRUE,
...
)

Arguments
x An object of class meta, or estimated treatment effect in individual studies.
left A logical indicating whether studies are supposed to be missing on the left or
right side of the funnel plot. If NULL, the linear regression test for funnel plot
symmetry (i.e., function metabias(...,method="Egger")) is used to deter-
mine whether studies are missing on the left or right side.
ma.fixed A logical indicating whether a fixed effect or random effects model is used to
estimate the number of missing studies.
type A character indicating which method is used to estimate the number of missing
studies. Either "L" or "R".
n.iter.max Maximum number of iterations to estimate number of missing studies.
level The level used to calculate confidence intervals for individual studies. If exist-
ing, x$level is used as value for level; otherwise 0.95 is used.
level.ma The level used to calculate confidence interval for the pooled estimate. If exist-
ing, x$level.ma is used as value for level.ma; otherwise 0.95 is used.
fixed A logical indicating whether a fixed effect meta-analysis should be conducted.
224 trimfill.meta

random A logical indicating whether a random effects meta-analysis should be con-

ducted.
hakn A logical indicating whether the method by Hartung and Knapp should be used
to adjust test statistics and confidence intervals.
method.tau A character string indicating which method is used to estimate the between-
study variance τ 2 and its square root τ . Either "DL", "PM", "REML", "ML", "HS",
"SJ", "HE", or "EB", can be abbreviated.
method.tau.ci A character string indicating which method is used to estimate the confidence
interval of τ 2 and τ . Either "QP", "BJ", or "J", or "", can be abbreviated.
prediction A logical indicating whether a prediction interval should be printed.
level.predict The level used to calculate prediction interval for a new study.
backtransf A logical indicating whether results should be back transformed in printouts and
plots. If backtransf=TRUE, results for sm="OR" are printed as odds ratios rather
than log odds ratios and results for sm="ZCOR" are printed as correlations rather
than Fisher’s z transformed correlations, for example.
pscale A numeric giving scaling factor for printing of single event probabilities or risk
differences, i.e. if argument sm is equal to "PLOGIT", "PLN", "PRAW", "PAS",
"PFT", or "RD".
irscale A numeric defining a scaling factor for printing of single incidence rates or in-
cidence rate differences, i.e. if argument sm is equal to "IR", "IRLN", "IRS",
"IRFT", or "IRD".
irunit A character specifying the time unit used to calculate rates, e.g. person-years.
silent A logical indicating whether basic information on iterations shown.
... other arguments
seTE Standard error of estimated treatment effect.
sm An optional character string indicating underlying summary measure, e.g., "RD",
"RR", "OR", "ASD", "HR", "MD", "SMD", or "ROM"; ignored if x is of class meta.
studlab An optional vector with study labels; ignored if x is of class meta.

Details
The trim-and-fill method (Duval, Tweedie 2000a, 2000b) can be used for estimating and adjusting
for the number and outcomes of missing studies in a meta-analysis. The method relies on scrutiny
of one side of a funnel plot for asymmetry assumed due to publication bias.
Three different methods have been proposed originally to estimate the number of missing studies.
Two of these methods (L- and R-estimator) have been shown to perform better in simulations, and
are available in this R function (argument type).
A fixed effect or random effects model can be used to estimate the number of missing studies
(argument ma.fixed). Furthermore, a fixed effect and/or random effects model can be used to
summaries study results (arguments fixed and random). Simulation results (Peters et al. 2007)
indicate that the fixed-random model, i.e. using a fixed effect model to estimate the number of
missing studies and a random effects model to summaries results, (i) performs better than the fixed-
fixed model, and (ii) performs no worse than and marginally better in certain situations than the
random-random model. Accordingly, the fixed-random model is the default.
trimfill.meta 225

An empirical comparison of the trim-and-fill method and the Copas selection model (Schwarzer
et al. 2010) indicates that the trim-and-fill method leads to excessively conservative inference in
practice. The Copas selection model is available in R package metasens.
The function metagen is called internally.

Value
An object of class c("metagen","meta","trimfill"). The object is a list containing the follow-
ing components:
studlab, sm, left, ma.fixed, type, n.iter.max
As defined above.
level, level.ma, level.predict
As defined above.
fixed, random, prediction
As defined above.
hakn, method.tau, method.tau.ci,
As defined above.
TE, seTE Estimated treatment effect and standard error of individual studies.
lower, upper Lower and upper confidence interval limits for individual studies.
statistic, pval
Statistic and p-value for test of treatment effect for individual studies.
w.fixed, w.random
Weight of individual studies (in fixed and random effects model).
TE.fixed, seTE.fixed
Estimated overall treatment effect and standard error (fixed effect model).
TE.random, seTE.random
Estimated overall treatment effect and standard error (random effects model).
seTE.predict Standard error utilised for prediction interval.
lower.predict, upper.predict
Lower and upper limits of prediction interval.
k Number of studies combined in meta-analysis.
Q Heterogeneity statistic Q.
tau Square-root of between-study variance.
method Pooling method: "Inverse".
call Function call.
n.iter Actual number of iterations to estimate number of missing studies.
trimfill A logical vector indicating studies that have been added by trim-and-fill method.
df.hakn Degrees of freedom for test of treatment effect for Hartung-Knapp method (only
if hakn=TRUE).
title Title of meta-analysis / systematic review.
complab Comparison label.
outclab Outcome label.
226 trimfill.meta

label.e Label for experimental group.

label.c Label for control group.
label.left Graph label on left side of forest plot.
label.right Graph label on right side of forest plot.
k0 Number of studies added by trim-and-fill.
n.e Number of observations in experimental group (only for object x of class metabin
or metacont).
n.c Number of observations in control group (only for object x of class metabin or
metacont).
event.e Number of events in experimental group (only for object x of class metabin).
event.c Number of events in control group (only for object x of class metabin).
mean.e Estimated mean in experimental group (only for object x of class metacont).
sd.e Standard deviation in experimental group (only for object x of class metacont).
mean.c Estimated mean in control group (only for object x of class metacont).
sd.c Standard deviation in control group (only for object x of class metacont).
n Number of observations (only for object x of class metaprop).
event Number of events (only for object x of class metaprop).
cor Corelation (only for object x of class metacor).
class.x Main class of object x (e.g. ’metabin’ or ’metacont’).
version Version of R package meta used to create object.

Author(s)
Guido Schwarzer <[email protected]>

References
Duval S & Tweedie R (2000a): A nonparametric "Trim and Fill" method of accounting for publica-
tion bias in meta-analysis. Journal of the American Statistical Association, 95, 89–98
Duval S & Tweedie R (2000b): Trim and Fill: A simple funnel-plot-based method of testing and
adjusting for publication bias in meta-analysis. Biometrics, 56, 455–63
Peters JL, Sutton AJ, Jones DR, Abrams KR, Rushton L (2007): Performance of the trim and fill
method in the presence of publication bias and between-study heterogeneity. Statisics in Medicine,
10, 4544–62
Schwarzer G, Carpenter J, Rücker G (2010): Empirical evaluation suggests Copas selection model
preferable to trim-and-fill method for selection bias in meta-analysis Journal of Clinical Epidemi-
ology, 63, 282–8

See Also
metagen, metabias, funnel
update.meta 227

Examples
data(Fleiss1993bin)
m1 <- metabin(d.asp, n.asp, d.plac, n.plac, data = Fleiss1993bin, sm = "OR")
tf1 <- trimfill(m1)
tf1
funnel(tf1)
funnel(tf1, pch = ifelse(tf1$trimfill, 1, 16), level = 0.9, random = FALSE)
#
# Use log odds ratios on x-axis
#
funnel(tf1, backtransf = FALSE)
funnel(tf1, pch = ifelse(tf1$trimfill, 1, 16), level = 0.9, random = FALSE,
backtransf = FALSE)

trimfill(m1$TE, m1$seTE, sm = m1$sm)

update.meta Update a meta-analysis object

Description
Update an existing meta-analysis object.

Usage
## S3 method for class 'meta'
update(
object,
data = object$data,
subset,
studlab,
exclude,
id,
method = object$method,
sm = object$sm,
incr,
allincr = object$allincr,
addincr = object$addincr,
allstudies = object$allstudies,
MH.exact = object$MH.exact,
RR.Cochrane = object$RR.Cochrane,
Q.Cochrane = object$Q.Cochrane,
model.glmm = object$model.glmm,
level = object$level,
level.ma = object$level.ma,
fixed = object$fixed,
random = object$random,
228 update.meta

overall = object$overall,
overall.hetstat = object$overall.hetstat,
hakn = object$hakn,
adhoc.hakn = object$adhoc.hakn,
method.tau = object$method.tau,
method.tau.ci = object$method.tau.ci,
tau.preset = object$tau.preset,
TE.tau = object$TE.tau,
tau.common = object$tau.common,
prediction = object$prediction,
level.predict = object$level.predict,
null.effect = object$null.effect,
method.bias = object$method.bias,
backtransf = object$backtransf,
pscale = object$pscale,
irscale = object$irscale,
irunit = object$irunit,
text.fixed = object$text.fixed,
text.random = object$text.random,
text.predict = object$text.predict,
text.w.fixed = object$text.w.fixed,
text.w.random = object$text.w.random,
title = object$title,
complab = object$complab,
outclab = object$outclab,
label.e = object$label.e,
label.c = object$label.c,
label.left = object$label.left,
label.right = object$label.right,
n.e = object$n.e,
n.c = object$n.c,
pooledvar = object$pooledvar,
method.smd = object$method.smd,
sd.glass = object$sd.glass,
exact.smd = object$exact.smd,
method.ci = object$method.ci,
subgroup,
subgroup.name = object$subgroup.name,
print.subgroup.name = object$print.subgroup.name,
sep.subgroup = object$sep.subgroup,
test.subgroup = object$test.subgroup,
prediction.subgroup = object$prediction.subgroup,
byvar,
print.CMH = object$print.CMH,
keepdata = TRUE,
left = object$left,
ma.fixed = object$ma.fixed,
type = object$type,
update.meta 229

n.iter.max = object$n.iter.max,
warn = FALSE,
warn.deprecated = gs("warn.deprecated"),
control = object$control,
...
)

Arguments
object An object of class meta.
data Dataset.
subset Subset.
studlab Study label.
exclude An optional vector specifying studies to exclude from meta-analysis, however,
to include in printouts and forest plots.
id An optional vector specifying which estimates come from the same study result-
ing in the use of a three-level meta-analysis model.
method A character string indicating which method is to be used for pooling of studies;
see metabin and metainc function for admissible values.
sm A character string indicating which summary measure is used for pooling.
incr Either a numerical value or vector which can be added to each cell frequency
for studies with a zero cell count or the character string "TA" which stands for
treatment arm continuity correction.
allincr A logical indicating if incr is added to each cell frequency of all studies if at
least one study has a zero cell count. If FALSE (default), incr is added only to
each cell frequency of studies with a zero cell count.
addincr A logical indicating if incr is added to each cell frequency of all studies irre-
spective of zero cell counts.
allstudies A logical indicating if studies with zero or all events in both groups are to be
included in the meta-analysis (applies only if sm is equal to "RR" or "OR").
MH.exact A logical indicating if incr is not to be added to all cell frequencies for studies
with a zero cell count to calculate the pooled estimate based on the Mantel-
Haenszel method.
RR.Cochrane A logical indicating if 2*incr instead of 1*incr is to be added to n.e and n.c
in the calculation of the risk ratio (i.e., sm="RR") for studies with a zero cell.
This is used in RevMan 5, the program for preparing and maintaining Cochrane
reviews.
Q.Cochrane A logical indicating if the Mantel-Haenszel estimate is used in the calculation of
the heterogeneity statistic Q which is implemented in RevMan 5, the program
for preparing and maintaining Cochrane reviews.
model.glmm A character string indicating which GLMM model should be used.
level The level used to calculate confidence intervals for individual studies.
level.ma The level used to calculate confidence intervals for pooled estimates.
230 update.meta

fixed A logical indicating whether a fixed effect meta-analysis should be conducted.

random A logical indicating whether a random effects meta-analysis should be con-
ducted.
overall A logical indicating whether overall summaries should be reported. This argu-
ment is useful in a meta-analysis with subgroups if overall results should not be
reported.
overall.hetstat
A logical value indicating whether to print heterogeneity measures for overall
treatment comparisons. This argument is useful in a meta-analysis with sub-
groups if heterogeneity statistics should only be printed on subgroup level.
hakn A logical indicating whether the method by Hartung and Knapp should be used
to adjust test statistics and confidence intervals.
adhoc.hakn A character string indicating whether an ad hoc variance correction should be
applied in the case of an arbitrarily small Hartung-Knapp variance estimate.
method.tau A character string indicating which method is used to estimate the between-
study variance τ 2 and its square root τ . Either "DL", "PM", "REML", "ML", "HS",
"SJ", "HE", or "EB", can be abbreviated. See function metagen.
method.tau.ci A character string indicating which method is used to estimate the confidence
interval of τ 2 and τ . Either "QP", "BJ", or "J", can be abbreviated.
tau.preset Prespecified value for the square root of the between-study variance τ 2 .
TE.tau Overall treatment effect used to estimate the between-study variance τ 2 .
tau.common A logical indicating whether tau-squared should be the same across subgroups.
prediction A logical indicating whether a prediction interval should be printed.
level.predict The level used to calculate prediction interval for a new study.
null.effect A numeric value specifying the effect under the null hypothesis.
method.bias A character string indicating which test for funnel plot asymmetry is to be used,
can be abbreviated. See function metabias.
backtransf A logical indicating whether results should be back transformed in printouts
and plots. If backtransf = TRUE, results for sm = "OR" are printed as odds ratios
rather than log odds ratios and results for sm = "ZCOR" are printed as correlations
rather than Fisher’s z transformed correlations, for example.
pscale A numeric giving scaling factor for printing of single event probabilities or risk
differences, i.e. if argument sm is equal to "PLOGIT", "PLN", "PRAW", "PAS",
"PFT", or "RD".
irscale A numeric defining a scaling factor for printing of single incidence rates or in-
cidence rate differences, i.e. if argument sm is equal to "IR", "IRLN", "IRS",
"IRFT", or "IRD".
irunit A character specifying the time unit used to calculate rates, e.g. person-years.
text.fixed A character string used in printouts and forest plot to label the pooled fixed effect
estimate.
text.random A character string used in printouts and forest plot to label the pooled random
effects estimate.
update.meta 231

text.predict A character string used in printouts and forest plot to label the prediction inter-
val.
text.w.fixed A character string used to label weights of fixed effect model.
text.w.random A character string used to label weights of random effects model.
title Title of meta-analysis / systematic review.
complab Comparison label.
outclab Outcome label.
label.e Label for experimental group.
label.c Label for control group.
label.left Graph label on left side of forest plot.
label.right Graph label on right side of forest plot.
n.e Number of observations in experimental group. (only for metagen object)
n.c Number of observations in control group. (only for metagen object)
pooledvar A logical indicating if a pooled variance should be used for the mean difference
(only for metacont object with sm = "MD").
method.smd A character string indicating which method is used to estimate the standardised
mean difference (only for metacont object with sm = "SMD"). Either "Hedges"
for Hedges’ g (default), "Cohen" for Cohen’s d, or "Glass" for Glass’ delta, can
be abbreviated.
sd.glass A character string indicating which standard deviation is used in the denomi-
nator for Glass’ method to estimate the standardised mean difference (only for
metacont object with sm = "SMD"). Either "control" using the standard devia-
tion in the control group (sd.c) or "experimental" using the standard deviation
in the experimental group (sd.e), can be abbreviated.
exact.smd A logical indicating whether exact formulae should be used in estimation of the
standardised mean difference and its standard error.
method.ci A character string indicating which method is used to calculate confidence inter-
vals for individual studies. Either "z", "t", "WS", "WSCC", "AC", "SA", "SACC",
or "NAsm", can be abbreviated. See functions metacont and metaprop.
subgroup An optional vector to conduct a meta-analysis with subgroups.
subgroup.name A character string with a name for the subgroup variable.
print.subgroup.name
A logical indicating whether the name of the subgroup variable should be printed
in front of the group labels.
sep.subgroup A character string defining the separator between name of subgroup variable and
subgroup label.
test.subgroup A logical value indicating whether to print results of test for subgroup differ-
ences.
prediction.subgroup
A logical indicating whether prediction intervals should be printed for sub-
groups.
byvar Deprecated argument (replaced by ’subgroup’).
232 update.meta

print.CMH A logical indicating whether result of the Cochran-Mantel-Haenszel test for

overall effect should be printed.
keepdata A logical indicating whether original data (set) should be kept in meta object.
left A logical indicating whether studies are supposed to be missing on the left or
right side of the funnel plot. If NULL, the linear regression test for funnel plot
symmetry (i.e., function metabias(...,method = "linreg")) is used to deter-
mine whether studies are missing on the left or right side.
ma.fixed A logical indicating whether a fixed effect or random effects model is used to
estimate the number of missing studies.
type A character indicating which method is used to estimate the number of missing
studies. Either "L" or "R".
n.iter.max Maximum number of iterations to estimate number of missing studies.
warn A logical indicating whether warnings should be printed (e.g., if incr is added
to studies with zero cell frequencies).
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
control An optional list to control the iterative process to estimate the between-study
variance τ 2 . This argument is passed on to rma.uni or rma.glmm, respectively.
... Additional arguments (ignored at the moment).

Details
Wrapper function to update an existing meta-analysis object which was created with R function
metabin, metacont, metacor, metagen, metainc, metamean, metaprop, or metarate. More de-
tails on function arguments are available in help files of respective R functions
This function can also be used for objects of class ’trimfill’, ’metacum’, and ’metainf’.

Value
An object of class "meta" and "metabin", "metacont", "metacor", "metainc", "metagen",
"metamean", "metaprop", or "metarate".

Author(s)
Guido Schwarzer <[email protected]>

See Also
metabin, metacont, metacor, metagen, metainc, metamean, metaprop, metarate

Examples
data(Fleiss1993cont)
m1 <- metacont(n.psyc, mean.psyc, sd.psyc, n.cont, mean.cont, sd.cont,
data = Fleiss1993cont, studlab = paste(study, year), sm = "SMD")
m1
weights.meta 233

# Change summary measure (from 'SMD' to 'MD')

#
update(m1, sm = "MD")

# Restrict analysis to subset of studies

#
update(m1, subset = 1:2)

# Use different levels for confidence intervals

#
m2 <- update(m1, level = 0.66, level.ma = 0.99)
print(m2, digits = 2)
forest(m2)

weights.meta Calculate absolute and percentage weights for meta-analysis

Description
This function returns a data frame containing information on absolute and percentage weights of
individual studies contributing to fixed effect and random effects meta-analysis.

Usage
## S3 method for class 'meta'
weights(
object,
fixed = object$fixed,
random = object$random,
warn.deprecated = gs("warn.deprecated"),
...
)

Arguments
object An object of class meta.
fixed A logical indicating whether absolute and percentage weights from the fixed
effect model should be calculated.
random A logical indicating whether absolute and percentage weights from the random
effects model should be calculated.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
... Additional arguments (to catch deprecated arguments).
234 weights.meta

Value
A data frame with the following variables is returned:
woodyplants 235

Variable Definition Condition

w.fixed absolute weights in fixed effect model (if fixed = TRUE)
p.fixed percentage weights in fixed effect model (if fixed = TRUE)
w.random absolute weights in random effects model (if random = TRUE)
p.random percentage weights in random effects model (if random = TRUE)

Author(s)
Guido Schwarzer <[email protected]>

# Print weights for fixed effect and random effects meta-analysis

#
weights(meta1)

# Do meta-analysis (only random effects model)

#
meta2 <- update(meta1, fixed = FALSE)

# Print weights for random effects meta-analysis

#
weights(meta2)

# Print weights for fixed effect and random effects meta-analysis

#
weights(meta2, fixed = TRUE)

woodyplants Elevated CO_2 and total biomass of woody plants

Description
Meta-analysis on effects of elevated CO_2 on total biomass of woody plants
This dataset has been used as an example in Hedges et al. (1999) to describe methods for the
meta-analysis of response ratios. The complete dataset with 102 observations and 26 variables is
available online as a supplement. Here only a subset of 10 variables is provided and used in the
examples.
236 woodyplants

Format
A data frame with the following columns:

obsno observation number

papno database paper number
treat treatment code
level treatment level
n.elev number of observations in experimental group (elevated CO_2-level)
mean.elev estimated mean in experimental group
sd.elev standard deviation in experimental group
n.amb number of observations in control group (ambient CO_2-level)
mean.amb estimated mean in control group
sd.amb standard deviation in control group

Source
Website http://www.esapubs.org/archive/ecol/E080/008/

References
Hedges LV, Gurevitch J, Curtis PS (1999): The meta-analysis of response ratios in experimental
ecology. Ecology, 80, 1150–6

Examples
data(woodyplants)

# Meta-analysis of response ratios (Hedges et al., 1999)

#
m1 <- metacont(n.elev, mean.elev, sd.elev, n.amb, mean.amb, sd.amb,
data = woodyplants, sm = "ROM", studlab = paste(obsno, papno, sep = " / "))
print(m1, prediction = TRUE)

# Meta-analysis for plants grown with low soil fertility treatment

#
m2 <- update(m1, subset = (treat == "fert" & level == "low"))
print(m2, prediction = TRUE)

# Meta-analysis for plants grown under low light conditions

#
m3 <- update(m1, subset = (treat == "light" & level == "low"))
print(m3, prediction = TRUE)
Index

∗ datagen bubble.metareg, 3, 11
longarm, 60
read.mtv, 206 ci, 14
read.rm5, 208 cilayout (print.meta), 196
∗ datasets cisapride, 15
amlodipine, 6 copas, 158
cisapride, 15
Fleiss1993bin, 21 dev.copy2eps, 37, 47
Fleiss1993cont, 21 dev.copy2pdf, 37, 47
Olkin1995, 192 drapery, 16
Pagliaro1992, 195
smoking, 218 Fleiss1993_CR (read.rm5), 208
woodyplants, 235 Fleiss1993bin, 21, 22
∗ hplot Fleiss1993cont, 21
baujat.meta, 8 Fleiss93 (Fleiss1993bin), 21
bubble.metareg, 11 Fleiss93cont (Fleiss1993cont), 21
drapery, 16 forest, 20, 82
forest.meta, 22 forest (forest.meta), 22
forest.metabind, 45 forest.meta, 3, 7, 22, 47, 53, 59, 105, 124,
funnel.meta, 48 152, 173, 214
labbe.metabin, 54 forest.metabind, 3, 41, 45, 85
radial.meta, 204 funnel, 67, 82, 205, 226
∗ htest funnel (funnel.meta), 48
metabias.rm5, 67 funnel.meta, 3, 48, 67
∗ models
metareg, 187 gpar, 33, 34
∗ package grid.xaxis, 30
meta-package, 3 gs, 52, 74, 91, 104, 120, 135, 150, 165, 180,
∗ print 212, 214
print.summary.meta, 201
∗ regression JAMAlabels, 53
metareg, 187
labbe (labbe.metabin), 54
amlodipine, 6 labbe.default, 3
as.data.frame.meta, 7 labbe.metabin, 3, 54
labels.meta, 4, 41, 53, 58, 212, 214
baujat (baujat.meta), 8 legend, 19
baujat.meta, 3, 8 limitmeta, 158
bubble, 188 longarm, 60
bubble (bubble.metareg), 11 lungcancer (smoking), 218

237
238 INDEX

meta (meta-package), 3 png, 37, 47

meta-package, 3 print.meta, 77, 82, 94, 105, 109, 115, 124,
metabias, 51, 68, 69, 72, 82, 90, 102, 118, 129, 138, 142, 145, 152, 168, 173,
134, 148, 163, 178, 205, 226, 230 182, 186, 196, 203, 214
metabias (metabias.meta), 62 print.metabias (metabias.meta), 62
metabias.meta, 3, 62 print.nnt.meta (nnt), 190
metabias.rm5, 3, 67, 200, 211, 221 print.rm5, 199, 211
metabin, 3, 4, 7, 15, 37, 39–41, 47, 51, 52, 58, print.summary.meta, 201, 220
61, 62, 67, 69, 99, 112, 113, 115, print.summary.rm5 (summary.rm5), 221
129, 142, 145, 158, 159, 164, 191,
194, 203, 205, 207, 211, 212, 217, radial, 20, 51
220, 229, 232, 235 radial (radial.meta), 204
metabind, 4, 46, 47, 84, 159, 160 radial.meta, 3, 204
metacont, 3, 6, 7, 36, 37, 39, 41, 47, 52, 61, read.mtv, 206
62, 67, 82, 86, 109, 112, 113, 115, read.rm5, 4, 69, 113, 200, 208, 221
129, 145, 149, 173, 186, 194, 203, rma.glmm, 69, 73, 74, 76, 80, 131, 135–137,
207, 211, 212, 217, 220, 231, 232, 141, 161, 164, 165, 167, 171, 176,
235 179–181, 185, 232
metacor, 3, 36, 37, 100, 212, 232 rma.mv, 116, 120
metacr, 4, 68, 69, 110, 200, 211, 212, 221 rma.uni, 63, 73, 91, 103, 120, 128, 135, 149,
metacum, 3, 37, 38, 113 164, 179, 187, 188, 232
metagen, 3, 4, 7, 10, 13, 37, 39, 41, 47, 51, 67, robu, 158
75, 76, 82, 85, 93, 94, 98, 99, 104,
105, 108, 109, 112, 113, 116, settings.meta, 4, 39, 41, 47, 52, 74, 91, 104,
136–138, 151, 152, 156, 158, 160, 113, 120, 124, 129, 135, 150, 165,
165, 166, 168, 173, 180, 182, 186, 180, 211
188, 191, 193, 194, 203, 205, 207, smd2or, 194, 215
211, 212, 216, 217, 220, 225, 226, smoking, 218
230, 232, 235 summary.meta, 188, 200, 203, 219, 221
metainc, 3, 4, 36, 37, 39, 61, 62, 131, 179, summary.rm5, 69, 211, 221
212, 218, 229, 232 svg, 37, 47
metainf, 3, 10, 13, 37, 38, 143
text, 9, 12, 50, 57
metamean, 3, 37, 146, 156, 232
to.long, 62
metamerge, 85, 157
trimfill, 158
metaprop, 3, 4, 37, 161, 212, 231, 232
trimfill (trimfill.meta), 222
metarate, 3, 4, 36, 37, 176, 212, 232
trimfill.default, 3
metareg, 3, 76, 82, 94, 105, 123, 137, 152, trimfill.meta, 3, 222
167, 181, 187
unit, 34
nnt, 190 update.meta, 74, 82, 91, 99, 104, 109, 120,
129, 135, 142, 150, 156, 165, 173,
Olkin1995, 192
180, 186, 203, 227
Olkin95 (Olkin1995), 192
or2smd, 193, 217 weights.meta, 233
weights.rma.mv, 120
Pagliaro1992, 195 woodyplants, 235
pairwise, 61, 62
par, 9, 19, 30
pdf, 37, 47

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