Package ‘adabag’

May 31, 2023

Type Package
Title Applies Multiclass AdaBoost.M1, SAMME and Bagging
Version 5.0
Date 2023-05-30
Author Alfaro, Esteban; Gamez, Matias and Garcia, Noelia; with contributions from L. Guo, A. Al-
bano, M. Sciandra and A. Plaia
Maintainer Esteban Alfaro <[email protected]>
Depends rpart, caret, foreach, doParallel, R (>= 4.0.0)
Imports methods, tidyr, dplyr, ConsRank (>= 2.1.3)
Suggests mlbench
Description It implements Freund and Schapire's Adaboost.M1 algorithm and Breiman's Bagging
algorithm using classification trees as individual classifiers. Once these classifiers have been
trained, they can be used to predict on new data. Also, cross validation estimation of the error can
be done. Since version 2.0 the function margins() is available to calculate the margins for these
classifiers. Also a higher flexibility is achieved giving access to the rpart.control() argument
of 'rpart'. Four important new features were introduced on version 3.0, AdaBoost-SAMME (Zhu
et al., 2009) is implemented and a new function errorevol() shows the error of the ensembles as
a function of the number of iterations. In addition, the ensembles can be pruned using the option
'newmfinal' in the predict.bagging() and predict.boosting() functions and the posterior probabil-
ity of
each class for observations can be obtained. Version 3.1 modifies the relative importance measure
to take into account the gain of the Gini index given by a variable in each tree and the weights of
these trees. Version 4.0 includes the margin-based ordered aggregation for Bagging pruning (Guo
and Boukir, 2013) and a function to auto prune the 'rpart' tree. Moreover, three new plots are also
available importanceplot(), plot.errorevol() and plot.margins(). Version 4.1 allows to predict on
unlabeled data. Version 4.2 includes the parallel computation option for some of the functions.
Version 5.0 includes the Boosting and Bagging algorithms for label ranking (Albano, Sciandra
and Plaia, 2023).
License GPL (>= 2)
Encoding UTF-8
LazyLoad yes
LazyData true

1
2 adabag-package

NeedsCompilation no
Repository CRAN
Date/Publication 2023-05-31 17:00:07 UTC

R topics documented:
adabag-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
autoprune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
bagging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
bagging.cv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
boosting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
boosting.cv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Ensemble_ranking_IW . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
errorevol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
errorevol_ranking_vector_IW . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
importanceplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
MarginOrderedPruning.Bagging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
margins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
plot.errorevol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
plot.margins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
predict.bagging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
predict.boosting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
prep_data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
simulatedRankingData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Index 34

adabag-package Applies Multiclass AdaBoost.M1, SAMME and Bagging

Description
It implements Freund and Schapire’s Adaboost.M1 algorithm and Breiman’s Bagging algorithm
using classification trees as individual classifiers. Once these classifiers have been trained, they
can be used to predict on new data. Also, cross validation estimation of the error can be done.
Since version 2.0 the function margins() is available to calculate the margins for these classifiers.
Also a higher flexibility is achieved giving access to the rpart.control() argument of ’rpart’. Four
important new features were introduced on version 3.0, AdaBoost-SAMME (Zhu et al., 2009) is
implemented and a new function errorevol() shows the error of the ensembles as a function of the
number of iterations. In addition, the ensembles can be pruned using the option ’newmfinal’ in
the predict.bagging() and predict.boosting() functions and the posterior probability of each class for
observations can be obtained. Version 3.1 modifies the relative importance measure to take into
account the gain of the Gini index given by a variable in each tree and the weights of these trees.
Version 4.0 includes the margin-based ordered aggregation for Bagging pruning (Guo and Boukir,
2013) and a function to auto prune the ’rpart’ tree. Moreover, three new plots are also available
importanceplot(), plot.errorevol() and plot.margins(). Version 4.1 allows to predict on unlabeled
adabag-package 3

data. Version 4.2 includes the parallel computation option for some of the functions. Version 5.0
includes the Boosting and Bagging algorithms for label ranking (Albano, Sciandra and Plaia, 2023).

Details

Package: adabag
Type: Package
Version: 5.0
Date: 2023-05-4
License: GPL(>= 2)
LazyLoad: yes

Author(s)
Author: Esteban Alfaro-Cortes, Matias Gamez-Martinez and Noelia Garcia-Rubio,
with contributions from L. Guo, A. Albano, M. Sciandra and A. Plaia
Maintainer: Esteban Alfaro-Cortes <[email protected]>

References
Albano, A., Sciandra, M., and Plaia, A. (2023): “A weighted distance-based approach with boosted
decision trees for label ranking”. Expert Systems with Applications.
Alfaro, E., Gamez, M. and Garcia, N. (2013): “adabag: An R Package for Classification with
Boosting and Bagging”. Journal of Statistical Software, 54(2), 1–35.
Alfaro, E., Garcia, N., Gamez, M. and Elizondo, D. (2008): “Bankruptcy forecasting: An empirical
comparison of AdaBoost and neural networks”. Decision Support Systems, 45, 110–122.
Breiman, L. (1998): “Arcing classifiers”. The Annals of Statistics, 26(3), 801–849.
Freund, Y. and Schapire, R.E. (1996): “Experiments with a new boosting algorithm”. In Proceed-
ings of the Thirteenth International Conference on Machine Learning, 148–156, Morgan Kaufmann.
Guo, L. and Boukir, S. (2013): "Margin-based ordered aggregation for ensemble pruning". Pattern
Recognition Letters, 34(6), 603-609.
Zhu, J., Zou, H., Rosset, S. and Hastie, T. (2009): “Multi-class AdaBoost”. Statistics and Its
Interface, 2, 349–360.

Reverse cites: To the best of our knowledge this package has been cited by:
Andriyas, S. and McKee, M. (2013). Recursive partitioning techniques for modeling irrigation
behavior. Environmental Modelling & Software, 47, 207–217.
Chan, J. C. W. and Paelinckx, D. (2008). Evaluation of Random Forest and Adaboost tree-based
ensemble classification and spectral band selection for ecotope mapping using airborne hyper-
spectral imagery. Remote Sensing of Environment, 112(6), 2999–3011.
Chrzanowska, M., Alfaro, E., and Witkowska, D. (2009). The individual borrowers recognition:
Single and ensemble trees. Expert Systems with Applications, 36(2), 6409–6414.
4 adabag-package

De Bock, K. W., Coussement, K., and Van den Poel, D. (2010). Ensemble classification based on
generalized additive models. Computational Statistics & Data Analysis, 54(6), 1535–1546.
De Bock, K. W. and Van den Poel, D. (2011). An empirical evaluation of rotation-based ensemble
classifiers for customer churn prediction. Expert Systems with Applications, 38(10), 12293–
12301.
Fan, Y., Murphy, T.B., William, R. and Watson G. (2009). digeR: GUI tool for analyzing 2D
DIGE data. R package version 1.2.
Garcia-Perez-de-Lema, D., Alfaro-Cortes, E., Manzaneque-Lizano, M. and Banegas-Ochovo, R.
(2012). Strategy, competitive factors and performance in small and medium enterprise (SMEs).
African Journal of Business Management, 6(26), 7714–7726.
Gonzalez-Rufino, E., Carrion, P., Cernadas, E., Fernandez-Delgado, M. and Dominguez-Petit, R.
(2013). Exhaustive comparison of colour texture features and classification methods to discrimi-
nate cells categories in histological images of fish ovary. Pattern Recognition, 46, 2391–2407.
Krempl, G. and Hofer, V. (2008). Partitioner trees: combining boosting and arbitrating. In: Okun,
O., Valentini, G. (eds.) Proc. 2nd Workshop Supervised and Unsupervised Ensemble Methods
and Their Applications, Patras, Greece, 61–66.
Maindonald, J. and Braun, J. (2010). Data Analysis and Graphics Using R - An Example-Based
Approach. 3rd ed, Cambridge University Press (p. 373)
Murphy, T. B., Dean, N. and Raftery, A. E. (2010). Variable selection and updating in model-
based discriminant analysis for high dimensional data with food authenticity applications. The
annals of applied statistics, 4(1), 396–421.
Stewart, B.M. and Zhukov, Y.M. (2009). Use of force and civil-military relations in Russia: An
automated content analysis. Small Wars & Insurgencies, 20(2), 319–343.
Torgo, L. (2010). Data Mining with R: Learning with Case Studies. Series: Chapman & Hall/CRC
Data Mining and Knowledge Discovery.
If you know any other work where this package is cited, please send us an email

See Also
autoprune, bagging, bagging.cv, boosting, boosting.cv, errorevol, importanceplot, margins,
MarginOrderedPruning.Bagging, plot.errorevol, plot.margins, predict.bagging, predict.boosting,
Ensemble_ranking_IW, errorevol_ranking_vector_IW, prep_data

Examples
## rpart library should be loaded
data(iris)
iris.adaboost <- boosting(Species~., data=iris, boos=TRUE,
mfinal=3)
importanceplot(iris.adaboost)

sub <- c(sample(1:50, 35), sample(51:100, 35), sample(101:150, 35))

iris.bagging <- bagging(Species ~ ., data=iris[sub,], mfinal=3)
#Predicting with labeled data
iris.predbagging<-predict.bagging(iris.bagging, newdata=iris[-sub,])
iris.predbagging
#Predicting with unlabeled data
iris.predbagging<- predict.bagging(iris.bagging, newdata=iris[-sub,-5])
iris.predbagging
autoprune 5

autoprune Builds automatically a pruned tree of class rpart

Description
Builds automatically a pruned tree of class rpart looking in the cptable for the minimum cross
validation error plus a standard deviation

Usage
autoprune(formula, data, subset=1:length(data[,1]), ...)

Arguments
formula a formula, as in the lm function.
data a data frame in which to interpret the variables named in the formula.
subset optional expression saying that only a subset of the rows of the data should be
used in the fit, as in the rpart function.
... further arguments passed to or from other methods.

Details
The cross validation estimation of the error (xerror) has a random component. To avoid this ran-
domness the 1-SE rule (or 1-SD rule) selects the simplest model with a xerror equal or less than the
minimum xerror plus the standard deviation of the minimum xerror.

Value
An object of class rpart

Author(s)
Esteban Alfaro-Cortes <[email protected]>, Matias Gamez-Martinez <[email protected]>
and Noelia Garcia-Rubio <[email protected]>

References
Breiman, L., Friedman, J.H., Olshen, R. and Stone, C.J. (1984): "Classification and Regression
Trees". Wadsworth International Group. Belmont
Therneau, T., Atkinson, B. and Ripley, B. (2014). rpart: Recursive Partitioning and Regression
Trees. R package version 4.1-5

See Also
rpart
6 bagging

Examples
## rpart library should be loaded
library(rpart)
data(iris)
iris.prune<-autoprune(Species~., data=iris)
iris.prune

## Comparing the test error of rpart and autoprune

library(mlbench)
data(BreastCancer)
l <- length(BreastCancer[,1])
sub <- sample(1:l,2*l/3)

BC.rpart <- rpart(Class~.,data=BreastCancer[sub,-1],cp=-1, maxdepth=5)

BC.rpart.pred <- predict(BC.rpart,newdata=BreastCancer[-sub,-1],type="class")
tb <-table(BC.rpart.pred,BreastCancer$Class[-sub])
tb
1-(sum(diag(tb))/sum(tb))

BC.prune<-autoprune(Class~.,data=BreastCancer[,-1],subset=sub)
BC.rpart.pred <- predict(BC.prune,newdata=BreastCancer[-sub,-1],type="class")
tb <-table(BC.rpart.pred,BreastCancer$Class[-sub])
tb
1-(sum(diag(tb))/sum(tb))

bagging Applies the Bagging algorithm to a data set

Description
Fits the Bagging algorithm proposed by Breiman in 1996 using classification trees as single classi-
fiers.

Usage
bagging(formula, data, mfinal = 100, control, par=FALSE,...)

Arguments
formula a formula, as in the lm function.
data a data frame in which to interpret the variables named in the formula
mfinal an integer, the number of iterations for which boosting is run or the number of
trees to use. Defaults to mfinal=100 iterations.
bagging 7

control options that control details of the rpart algorithm. See rpart.control for more
details.
par if TRUE, the cross validation process is runned in parallel. If FALSE (by default),
the function runs without parallelization.
... further arguments passed to or from other methods.

Details
Unlike boosting, individual classifiers are independent among them in bagging

Value
An object of class bagging, which is a list with the following components:

formula the formula used.

trees the trees grown along the iterations.
votes a matrix describing, for each observation, the number of trees that assigned it to
each class.
prob a matrix describing, for each observation, the posterior probability or degree of
support of each class. These probabilities are calculated using the proportion of
votes in the final ensemble.
class the class predicted by the ensemble classifier.
samples the bootstrap samples used along the iterations.
importance returns the relative importance of each variable in the classification task. This
measure takes into account the gain of the Gini index given by a variable in each
tree.

Author(s)
Esteban Alfaro-Cortes <[email protected]>, Matias Gamez-Martinez <[email protected]>
and Noelia Garcia-Rubio <[email protected]>

References
Alfaro, E., Gamez, M. and Garcia, N. (2013): “adabag: An R Package for Classification with
Boosting and Bagging”. Journal of Statistical Software, Vol 54, 2, pp. 1–35.
Alfaro, E., Garcia, N., Gamez, M. and Elizondo, D. (2008): “Bankruptcy forecasting: An empirical
comparison of AdaBoost and neural networks”. Decision Support Systems, 45, pp. 110–122.
Breiman, L. (1996): "Bagging predictors". Machine Learning, Vol 24, 2, pp.123–140.
Breiman, L. (1998): "Arcing classifiers". The Annals of Statistics, Vol 26, 3, pp. 801–849.

See Also
predict.bagging, bagging.cv
8 bagging.cv

Examples
## rpart library should be loaded
#This example has been hidden to fulfill execution time <5s
#library(rpart)
#data(iris)
#iris.bagging <- bagging(Species~., data=iris, mfinal=10)

# Data Vehicle (four classes)

library(rpart)
library(mlbench)
data(Vehicle)
l <- length(Vehicle[,1])
sub <- sample(1:l,2*l/3)
Vehicle.bagging <- bagging(Class ~.,data=Vehicle[sub, ],mfinal=5,
control=rpart.control(maxdepth=5, minsplit=15))
#Using the pruning option
Vehicle.bagging.pred <- predict.bagging(Vehicle.bagging,newdata=Vehicle[-sub, ], newmfinal=3)
Vehicle.bagging.pred$confusion
Vehicle.bagging.pred$error

bagging.cv Runs v-fold cross validation with Bagging

Description
The data are divided into v non-overlapping subsets of roughly equal size. Then, bagging is applied
on (v-1) of the subsets. Finally, predictions are made for the left out subsets, and the process is
repeated for each of the v subsets.

Usage
bagging.cv(formula, data, v = 10, mfinal = 100, control, par=FALSE)

Arguments
formula a formula, as in the lm function.
data a data frame in which to interpret the variables named in formula
v An integer, specifying the type of v-fold cross validation. Defaults to 10. If v is
set as the number of observations, leave-one-out cross validation is carried out.
Besides this, every value between two and the number of observations is valid
and means that roughly every v-th observation is left out.
mfinal an integer, the number of iterations for which boosting is run or the number of
trees to use. Defaults to mfinal=100 iterations.
control options that control details of the rpart algorithm. See rpart.control for more
details.
par if TRUE, the cross validation process is runned in parallel. If FALSE (by default),
the function runs without parallelization.
bagging.cv 9

Value

An object of class bagging.cv, which is a list with the following components:

class the class predicted by the ensemble classifier.

confusion the confusion matrix which compares the real class with the predicted one.
error returns the average error.

Author(s)

Esteban Alfaro-Cortes <[email protected]>, Matias Gamez-Martinez <[email protected]>

and Noelia Garcia-Rubio <[email protected]>

References

Alfaro, E., Gamez, M. and Garcia, N. (2013): “adabag: An R Package for Classification with
Boosting and Bagging”. Journal of Statistical Software, Vol 54, 2, pp. 1–35.
Alfaro, E., Garcia, N., Gamez, M. and Elizondo, D. (2008): “Bankruptcy forecasting: An empirical
comparison of AdaBoost and neural networks”. Decision Support Systems, 45, pp. 110–122.
Breiman, L. (1996): "Bagging predictors". Machine Learning, Vol 24, 2, pp. 123–140.
Breiman, L. (1998). "Arcing classifiers". The Annals of Statistics, Vol 26, 3, pp. 801–849.

See Also

bagging, predict.bagging

Examples
## rpart library should be loaded
library(rpart)
data(iris)
iris.baggingcv <- bagging.cv(Species ~ ., v=2, data=iris, mfinal=3,
control=rpart.control(cp=0.01))
iris.baggingcv[-1]

## rpart and mlbench libraries should be loaded

## Data Vehicle (four classes)
#This example has been hidden to keep execution time <5s
#data(Vehicle)
#Vehicle.bagging.cv <- bagging.cv(Class ~.,data=Vehicle,v=5,mfinal=10,
#control=rpart.control(maxdepth=5))
#Vehicle.bagging.cv[-1]
10 boosting

boosting Applies the AdaBoost.M1 and SAMME algorithms to a data set

Description
Fits the AdaBoost.M1 (Freund and Schapire, 1996) and SAMME (Zhu et al., 2009) algorithms
using classification trees as single classifiers.

Usage
boosting(formula, data, boos = TRUE, mfinal = 100, coeflearn = 'Breiman',
control,...)

Arguments
formula a formula, as in the lm function.
data a data frame in which to interpret the variables named in formula.
boos if TRUE (by default), a bootstrap sample of the training set is drawn using the
weights for each observation on that iteration. If FALSE, every observation is
used with its weights.
mfinal an integer, the number of iterations for which boosting is run or the number of
trees to use. Defaults to mfinal=100 iterations.
coeflearn if ’Breiman’(by default), alpha=1/2ln((1-err)/err) is used. If ’Freund’
alpha=ln((1-err)/err) is used. In both cases the AdaBoost.M1 algorithm
is used and alpha is the weight updating coefficient. On the other hand, if co-
eflearn is ’Zhu’ the SAMME algorithm is implemented with alpha=ln((1-err)/err)+
ln(nclasses-1).
control options that control details of the rpart algorithm. See rpart.control for more
details.
... further arguments passed to or from other methods.

Details
AdaBoost.M1 and SAMME are simple generalizations of AdaBoost for more than two classes. In
AdaBoost-SAMME the individual trees are required to have an error lower than 1-1/nclasses instead
of 1/2 of the AdaBoost.M1

Value
An object of class boosting, which is a list with the following components:

formula the formula used.

trees the trees grown along the iterations.
weights a vector with the weighting of the trees of all iterations.
boosting 11

votes a matrix describing, for each observation, the number of trees that assigned it to
each class, weighting each tree by its alpha coefficient.
prob a matrix describing, for each observation, the posterior probability or degree of
support of each class. These probabilities are calculated using the proportion of
votes in the final ensemble.
class the class predicted by the ensemble classifier.
importance returns the relative importance of each variable in the classification task. This
measure takes into account the gain of the Gini index given by a variable in a
tree and the weight of this tree.

Author(s)
Esteban Alfaro-Cortes <[email protected]>, Matias Gamez-Martinez <[email protected]>
and Noelia Garcia-Rubio <[email protected]>

References
Alfaro, E., Gamez, M. and Garcia, N. (2013): “adabag: An R Package for Classification with
Boosting and Bagging”. Journal of Statistical Software, Vol 54, 2, pp. 1–35.
Alfaro, E., Garcia, N., Gamez, M. and Elizondo, D. (2008): “Bankruptcy forecasting: An empirical
comparison of AdaBoost and neural networks”. Decision Support Systems, 45, pp. 110–122.
Breiman, L. (1998): “Arcing classifiers”. The Annals of Statistics, Vol 26, 3, pp. 801–849.
Freund, Y. and Schapire, R.E. (1996): “Experiments with a new boosting algorithm”. In Pro-
ceedings of the Thirteenth International Conference on Machine Learning, pp. 148–156, Morgan
Kaufmann.
Zhu, J., Zou, H., Rosset, S. and Hastie, T. (2009): “Multi-class AdaBoost”. Statistics and Its
Interface, 2, pp. 349–360.

See Also
predict.boosting, boosting.cv

Examples

## rpart library should be loaded

data(iris)
iris.adaboost <- boosting(Species~., data=iris, boos=TRUE, mfinal=3)
iris.adaboost

## Data Vehicle (four classes)

library(mlbench)
data(Vehicle)
l <- length(Vehicle[,1])
sub <- sample(1:l,2*l/3)
mfinal <- 3
maxdepth <- 5
12 boosting.cv

Vehicle.rpart <- rpart(Class~.,data=Vehicle[sub,],maxdepth=maxdepth)

Vehicle.rpart.pred <- predict(Vehicle.rpart,newdata=Vehicle[-sub, ],type="class")
tb <- table(Vehicle.rpart.pred,Vehicle$Class[-sub])
error.rpart <- 1-(sum(diag(tb))/sum(tb))
tb
error.rpart

Vehicle.adaboost <- boosting(Class ~.,data=Vehicle[sub, ],mfinal=mfinal, coeflearn="Zhu",

control=rpart.control(maxdepth=maxdepth))
Vehicle.adaboost.pred <- predict.boosting(Vehicle.adaboost,newdata=Vehicle[-sub, ])
Vehicle.adaboost.pred$confusion
Vehicle.adaboost.pred$error

#comparing error evolution in training and test set

errorevol(Vehicle.adaboost,newdata=Vehicle[sub, ])->evol.train
errorevol(Vehicle.adaboost,newdata=Vehicle[-sub, ])->evol.test

plot.errorevol(evol.test,evol.train)

boosting.cv Runs v-fold cross validation with AdaBoost.M1 or SAMME

Description
The data are divided into v non-overlapping subsets of roughly equal size. Then, boosting is
applied on (v-1) of the subsets. Finally, predictions are made for the left out subsets, and the
process is repeated for each of the v subsets.

Usage
boosting.cv(formula, data, v = 10, boos = TRUE, mfinal = 100,
coeflearn = "Breiman", control, par=FALSE)

Arguments
formula a formula, as in the lm function.
data a data frame in which to interpret the variables named in formula
boos if TRUE (by default), a bootstrap sample of the training set is drawn using the
weights for each observation on that iteration. If FALSE, every observation is
used with its weights.
v An integer, specifying the type of v-fold cross validation. Defaults to 10. If v is
set as the number of observations, leave-one-out cross validation is carried out.
Besides this, every value between two and the number of observations is valid
and means that roughly every v-th observation is left out.
boosting.cv 13

mfinal an integer, the number of iterations for which boosting is run or the number of
trees to use. Defaults to mfinal=100 iterations.
coeflearn if ’Breiman’(by default), alpha=1/2ln((1-err)/err) is used. If ’Freund’
alpha=ln((1-err)/err) is used. In both cases the AdaBoost.M1 algorithm
is used and alpha is the weight updating coefficient. On the other hand, if co-
eflearn is ’Zhu’ the SAMME algorithm is implemented with alpha=ln((1-err)/err)+
ln(nclasses-1).
control options that control details of the rpart algorithm. See rpart.control for more
details.
par if TRUE, the cross validation process is runned in parallel. If FALSE (by default),
the function runs without parallelization.

Value

An object of class boosting.cv, which is a list with the following components:

class the class predicted by the ensemble classifier.

confusion the confusion matrix which compares the real class with the predicted one.
error returns the average error.

Author(s)

Esteban Alfaro-Cortes <[email protected]>, Matias Gamez-Martinez <[email protected]>

and Noelia Garcia-Rubio <[email protected]>

References

Alfaro, E., Gamez, M. and Garcia, N. (2013): “adabag: An R Package for Classification with
Boosting and Bagging”. Journal of Statistical Software, Vol 54, 2, pp. 1–35.
Alfaro, E., Garcia, N., Gamez, M. and Elizondo, D. (2008): “Bankruptcy forecasting: An empirical
comparison of AdaBoost and neural networks”. Decision Support Systems, 45, pp. 110–122.
Breiman, L. (1998): "Arcing classifiers". The Annals of Statistics, Vol 26, 3, pp. 801–849.
Freund, Y. and Schapire, R.E. (1996): "Experiments with a new boosting algorithm". In Pro-
ceedings of the Thirteenth International Conference on Machine Learning, pp. 148–156, Morgan
Kaufmann.
Zhu, J., Zou, H., Rosset, S. and Hastie, T. (2009): “Multi-class AdaBoost”. Statistics and Its
Interface, 2, pp. 349–360.

See Also

boosting, predict.boosting
14 Ensemble_ranking_IW

Examples

## rpart library should be loaded

data(iris)
iris.boostcv <- boosting.cv(Species ~ ., v=2, data=iris, mfinal=5,
control=rpart.control(cp=0.01))
iris.boostcv[-1]

## rpart and mlbench libraries should be loaded

## Data Vehicle (four classes)
#This example has been hidden to fulfill execution time <5s
#data(Vehicle)
#Vehicle.boost.cv <- boosting.cv(Class ~.,data=Vehicle,v=5, mfinal=10, coeflearn="Zhu",
#control=rpart.control(maxdepth=5))
#Vehicle.boost.cv[-1]

Ensemble_ranking_IW Ensemble methods for ranking data: Item-Weighted Boosting and

Bagging Algorithms

Description

The Ensemble_ranking_IW function applies the item-weighted Boosting and Bagging algorithms
to ranking data (Albano et al., 2023). These algorithms utilize classification trees as base classifiers
to perform item-weighted ensemble methods for rankings.

Usage

Ensemble_ranking_IW(formula, data, iw, algo = "boosting",

mfinal = 100, coeflearn = "Breiman", control, bin = FALSE,
trace= TRUE, ...)

Arguments

formula a formula specifying the response ranking variable and predictors, similar to the
lm function. The response variable must be the "Label" column of the object
generated by the prep_data function.
data An N by (K+1) data frame containing the prepared item-weighted ranking data.
The column "Label" should contain the transformed ranking responses, and the
remaining columns should contain the predictors. Continuous variables are al-
lowed, while the dummy coding should be used for categorical variables. The
data frame must be the output of the prep_data function.
Ensemble_ranking_IW 15

iw a vector or matrix representing the item weights or dissimilarities for the ranking
data. For a vector, it should be a row vector of length M, where M is the number
of items. For a matrix, it should be a symmetric M by M matrix representing
item dissimilarities. For coherence, iw should be the same vector/matrix used in
prep_data(...).
algo the ensemble method to use. Possible values are "bagging" or "boosting". De-
faults to "boosting".
mfinal the number of trees to use for boosting or bagging. Defaults to 100 iterations.
coeflearn the coefficient learning method to use. Possible values are "Breiman", "Freund",
or "Zhu". Defaults to "Breiman".
control an optional argument to control details of the classification tree algorithm. See
rpart.control for more information.
bin a logical value indicating whether to use the binary logarithm function for up-
dating weights at each iteration. Defaults to FALSE. When set to TRUE, it cor-
responds to utilizing the AdaBoost.R.M2 algorithm as defined by Albano et al.
(2023).
trace a logical value controling the display of additional information ( the number of
trees and the average weighted tau_x) during execution. Defaults to TRUE.
... additional arguments passed to or from other methods.

Details
The Ensemble_ranking_IW function extends the Boosting and Bagging algorithms to handle item-
weighted ranking data. It allows for the application of these ensemble methods to improve ranking
predicting performance using classification trees as base classifiers.

Value
An object of class boosting or bagging, which is a list with the following components:
formula the used formula.
trees the trees grown during the iterations.
weights a vector of weights for each tree in all iterations.
importance a measure of the relative importance of each predictor in the ranking task, taking
into account the weighted gain of the variable’s contribution in each tree.

Author(s)
Alessandro Albano <[email protected]>, Mariangela Sciandra <[email protected]>,
and Antonella Plaia <[email protected]>

References
Albano, A., Sciandra, M., and Plaia, A. (2023): "A weighted distance-based approach with boosted
decision trees for label ranking." Expert Systems with Applications.
Alfaro, E., Gamez, M., and Garcia, N. (2013): "adabag: An R Package for Classification with
Boosting and Bagging." Journal of Statistical Software, Vol. 54, 2, pp. 1–35.
16 Ensemble_ranking_IW

Breiman, L. (1998): "Arcing classifiers." The Annals of Statistics, Vol. 26, 3, pp. 801–849.
D’Ambrosio, A.[aut, cre], Amodio, S. [ctb], Mazzeo, G. [ctb], Albano, A. [ctb], Plaia, A. [ctb]
(2023). ConsRank: Compute the Median Ranking(s) According to the Kemeny’s Axiomatic Ap-
proach. R package version 2.1.3, https://cran.r-project.org/package=ConsRank.
Freund, Y., and Schapire, R.E. (1996): "Experiments with a new boosting algorithm." In Pro-
ceedings of the Thirteenth International Conference on Machine Learning, pp. 148–156, Morgan
Kaufmann.
Plaia, A., Buscemi, S., Furnkranz, J., and Mencıa, E.L. (2021): "Comparing boosting and bagging
for decision trees of rankings." Journal of Classification, pages 1–22.
Zhu, J., Zou, H., Rosset, S., and Hastie, T. (2009): "Multi-class AdaBoost." Statistics and Its
Interface, 2, pp. 349–360.

Examples
## Not run:
# Load simulated ranking data
data(simulatedRankingData)
x <- simulatedRankingData$x
y <- simulatedRankingData$y

# Prepare the data with item weights

dati <- prep_data(y, x, iw = c(2, 5, 5, 2))

# Divide the data into training and test sets

set.seed(12345)
samp <- sample(nrow(dati))
l <- length(dati[, 1])
sub <- sample(1:l, 2 * l / 3)
data_sub1 <- dati[sub, ]
data_test1 <- dati[-sub, ]

# Apply ensemble ranking with AdaBoost.M1

boosting_1 <- Ensemble_ranking_IW(
Label ~ .,
data = data_sub1,
iw = c(2, 5, 5, 2),
mfinal = 3,
coeflearn = "Breiman",
control = rpart.control(maxdepth = 4, cp = -1),
algo = "boosting",
bin = FALSE
)

# Evaluate the performance

test_boosting1 <- errorevol_ranking_vector_IW(boosting_1,
newdata = data_test1, iw=c(2,5,5,2), squared = FALSE)
test_boosting1.1 <- errorevol_ranking_vector_IW(boosting_1,
newdata = data_sub1, iw=c(2,5,5,2), squared = FALSE)

# Plot the error evolution

plot.errorevol(test_boosting1, test_boosting1.1)
errorevol 17

## End(Not run)

errorevol Shows the error evolution of the ensemble

Description
Calculates the error evolution of an AdaBoost.M1, AdaBoost-SAMME or Bagging classifier for a
data frame as the ensemble size grows

Usage
errorevol(object, newdata)

Arguments
object This object must be the output of one of the functions bagging or boosting.
This is assumed to be the result of some function that produces an object with
two components named formula and trees, as those returned for instance by
the bagging function.
newdata Could be the same data frame used in object or a new one

Details
This can be useful to see how fast Bagging, boosting reduce the error of the ensemble. in addition,
it can detect the presence of overfitting and, therefore, the convenience of pruning the ensemble
using predict.bagging or predict.boosting.

Value
An object of class errorevol, which is a list with only one component:

error a vector with the error evolution.

Author(s)
Esteban Alfaro-Cortes <[email protected]>, Matias Gamez-Martinez <[email protected]>
and Noelia Garcia-Rubio <[email protected]>

References
Alfaro, E., Gamez, M. and Garcia, N. (2013): “adabag: An R Package for Classification with
Boosting and Bagging”. Journal of Statistical Software, Vol 54, 2, pp. 1–35.
Alfaro, E., Garcia, N., Gamez, M. and Elizondo, D. (2008): “Bankruptcy forecasting: An empirical
comparison of AdaBoost and neural networks”. Decision Support Systems, 45, pp. 110–122.
Breiman, L. (1996): “Bagging predictors”. Machine Learning, Vol 24, 2, pp.123–140.
18 errorevol_ranking_vector_IW

Freund, Y. and Schapire, R.E. (1996): “Experiments with a new boosting algorithm”. In Pro-
ceedings of the Thirteenth International Conference on Machine Learning, pp. 148–156, Morgan
Kaufmann.
Zhu, J., Zou, H., Rosset, S. and Hastie, T. (2009): “Multi-class AdaBoost”. Statistics and Its
Interface, 2, pp. 349–360.

See Also

boosting, predict.boosting, bagging, predict.bagging

Examples

library(mlbench)
data(BreastCancer)
l <- length(BreastCancer[,1])
sub <- sample(1:l,2*l/3)
cntrl <- rpart.control(maxdepth = 3, minsplit = 0, cp = -1)

BC.adaboost <- boosting(Class ~.,data=BreastCancer[sub,-1],mfinal=5, control=cntrl)

BC.adaboost.pred <- predict.boosting(BC.adaboost,newdata=BreastCancer[-sub,-1])

errorevol(BC.adaboost,newdata=BreastCancer[-sub,-1])->evol.test
errorevol(BC.adaboost,newdata=BreastCancer[sub,-1])->evol.train

plot.errorevol(evol.test,evol.train)
abline(h=min(evol.test[[1]]), col="red",lty=2,lwd=2)
abline(h=min(evol.train[[1]]), col="blue",lty=2,lwd=2)

errorevol_ranking_vector_IW
Calculate the error evolution and final predictions of an item-weighted
ensemble for rankings

Description

This function calculates the error evolution and final predictions of an item-weigthed ensemble
method for ranking data (Albano et al., 2023).

Usage

errorevol_ranking_vector_IW(object, newdata, iw, squared = FALSE)

errorevol_ranking_vector_IW 19

Arguments

object an object of class ’bagging’ or ’boosting’ generated by the Ensemble_ranking_IW

function.
newdata a data frame that can be the same as the one used in the object or a new one.
Continuous variables are allowed, while the dummy coding should be used for
categorical variables. It must be the output of the prep_data function.
iw a weighting vector or matrix. For coherence, iw should be the same vector/matrix
used in Ensemble_ranking_IW(...).
squared logical value indicating whether squared weighting should be used in the final
prediction. Default is FALSE. When set to TRUE, it corresponds to utilizing the
AdaBoost.R.M3 algorithm defined by Albano et al. (2023).

Details

This function computes the error and final predictions for a boosting or bagging ranking model
using item weighting.

Value

An object of class ’errorevol’. It has two components:

error a vector with the error values at each ensemble iteration

final_prediction
a data frame of final predictions for each observation in newdata.

References

Albano, A., Sciandra, M., and Plaia, A. (2023): "A weighted distance-based approach with boosted
decision trees for label ranking." Expert Systems with Applications.
Alfaro, E., Gamez, M., and Garcia, N. (2013): "adabag: An R Package for Classification with
Boosting and Bagging." Journal of Statistical Software, Vol. 54, 2, pp. 1–35.
Breiman, L. (1998): "Arcing classifiers." The Annals of Statistics, Vol. 26, 3, pp. 801–849.
D’Ambrosio, A.[aut, cre], Amodio, S. [ctb], Mazzeo, G. [ctb], Albano, A. [ctb], Plaia, A. [ctb]
(2023). ConsRank: Compute the Median Ranking(s) According to the Kemeny’s Axiomatic Ap-
proach. R package version 2.1.3, https://cran.r-project.org/package=ConsRank.
Freund, Y., and Schapire, R.E. (1996): "Experiments with a new boosting algorithm." In Pro-
ceedings of the Thirteenth International Conference on Machine Learning, pp. 148–156, Morgan
Kaufmann.
Plaia, A., Buscemi, S., Furnkranz, J., and Mencıa, E.L. (2021): "Comparing boosting and bagging
for decision trees of rankings." Journal of Classification, pages 1–22.
Zhu, J., Zou, H., Rosset, S., and Hastie, T. (2009): "Multi-class AdaBoost." Statistics and Its
Interface, 2, pp. 349–360.
20 importanceplot

Examples
## Not run:
# Load simulated ranking data
data(simulatedRankingData)
x <- simulatedRankingData$x
y <- simulatedRankingData$y

# Prepare the data with item weights

dati <- prep_data(y, x, iw = c(2, 5, 5, 2))

# Divide the data into training and test sets

set.seed(12345)
samp <- sample(nrow(dati))
l <- length(dati[, 1])
sub <- sample(1:l, 2 * l / 3)
data_sub1 <- dati[sub, ]
data_test1 <- dati[-sub, ]

# Apply ensemble ranking with AdaBoost.M1

boosting_1 <- Ensemble_ranking_IW(
Label ~ .,
data = data_sub1,
iw = c(2, 5, 5, 2),
mfinal = 3,
coeflearn = "Breiman",
control = rpart.control(maxdepth = 4, cp = -1),
algo = "boosting",
bin = FALSE
)

# Evaluate the performance

test_boosting1 <- errorevol_ranking_vector_IW(boosting_1,
newdata = data_test1, iw=c(2,5,5,2), squared = FALSE)
test_boosting1.1 <- errorevol_ranking_vector_IW(boosting_1,
newdata = data_sub1, iw=c(2,5,5,2), squared = FALSE)

# Plot the error evolution

plot.errorevol(test_boosting1, test_boosting1.1)

## End(Not run)

importanceplot Plots the variables relative importance

Description
Plots the relative importance of each variable in the classification task. This measure takes into
account the gain of the Gini index given by a variable in a tree and, in the boosting case, the weight
of this tree.
importanceplot 21

Usage
importanceplot(object, ...)

Arguments
object fitted model object of class boosting or bagging. This is assumed to be the re-
sult of some function that produces an object with a component named importance
as that returned by the boosting and bagging functions.
... further arguments passed to or from other methods.

Details
For this goal, the varImp function of the caret package is used to get the gain of the Gini index of
the variables in each tree.

Value
A labeled plot is produced on the current graphics device (one being opened if needed).

Author(s)
Esteban Alfaro-Cortes <[email protected]>, Matias Gamez-Martinez <[email protected]>
and Noelia Garcia-Rubio <[email protected]>

References
Alfaro, E., Gamez, M. and Garcia, N. (2013): “adabag: An R Package for Classification with
Boosting and Bagging”. Journal of Statistical Software, Vol 54, 2, pp. 1–35.
Alfaro, E., Garcia, N., Gamez, M. and Elizondo, D. (2008): “Bankruptcy forecasting: An empirical
comparison of AdaBoost and neural networks”. Decision Support Systems, 45, pp. 110–122.
Breiman, L. (1996): “Bagging predictors”. Machine Learning, Vol 24, 2, pp.123–140.
Freund, Y. and Schapire, R.E. (1996): “Experiments with a new boosting algorithm”. In Pro-
ceedings of the Thirteenth International Conference on Machine Learning, pp. 148–156, Morgan
Kaufmann.
Zhu, J., Zou, H., Rosset, S. and Hastie, T. (2009): “Multi-class AdaBoost”. Statistics and Its
Interface, 2, pp. 349–360.

See Also
boosting, bagging,

Examples
#Examples
#Iris example
library(rpart)
data(iris)
sub <- c(sample(1:50, 25), sample(51:100, 25), sample(101:150, 25))
22 MarginOrderedPruning.Bagging

iris.adaboost <- boosting(Species ~ ., data=iris[sub,], mfinal=3)

importanceplot(iris.adaboost)

#Examples with bagging

#iris.bagging <- bagging(Species ~ ., data=iris[sub,], mfinal=5)
#importanceplot(iris.bagging, horiz=TRUE, cex.names=.6)

MarginOrderedPruning.Bagging
MarginOrderedPruning.Bagging

Description
Margin-based ordered aggregation for bagging pruning

Usage
MarginOrderedPruning.Bagging(baggingObject, trainingset, pruningset,
marginType = "unsupervised", doTrace = TRUE)

Arguments
baggingObject fitted model object of class bagging
trainingset the training set of the bagging object
pruningset a set aside dataset for bagging pruning
marginType if "unsupervised" (by default) the margin is the difference between the propor-
tions of votes of the first and second most popular classes. Else the margin is
calculated as the difference between the proportion of votes of the correct class
and the most popular among the other classes
doTrace If set to TRUE, give a more verbose output as MarginOrderedPruning.Bagging
is running

Value
Returns a list with the following components:
prunedBagging a pruned bagging object
AccuracyOrderedEnsemblePruningSet
Accuracy of each ordered ensemble on pruning set

Note
Questions about this function should be sent to Li Guo

Author(s)
Li Guo <[email protected]>
margins 23

References

Guo, L. and Boukir, S. (2013): "Margin-based ordered aggregation for ensemble pruning". Pattern
Recognition Letters, 34(6), 603-609.

See Also

bagging, predict.bagging

Examples
## mlbench package should be loaded
library(mlbench)
data(Satellite)
## Separate data into 3 parts: training set, pruning set and test set
ind <- sample(3, nrow(Satellite), replace = TRUE, prob=c(0.3, 0.2,0.5))

## create bagging with training set

#increase mfinal in your own execution of this example to see
#the real usefulness of this function
Satellite.bagging<-bagging(classes~.,data=Satellite[ind==1,],mfinal=3)
#Satellite.bagging.pred<-predict(Satellite.bagging,Satellite[ind==3,])

##pruning bagging
Satellite.bagging.pruning<-MarginOrderedPruning.Bagging(Satellite.bagging,
Satellite[ind==1,],Satellite[ind==2,])
#Satellite.bagging.pruning.pred<-predict(Satellite.bagging.pruning$prunedBagging,
#Satellite[ind==3,])

## create bagging with training and pruning set

#This example has been hidden to fulfill execution time <5s
#Satellite.bagging2<-bagging(classes~.,data=Satellite[ind!=3,],25)
#Satellite.bagging2.pred<-predict(Satellite.bagging2,Satellite[ind==3,])

margins Calculates the margins

Description

Calculates the margins of an AdaBoost.M1, AdaBoost-SAMME or Bagging classifier for a data

frame

Usage

margins(object, newdata)
24 margins

Arguments
object This object must be the output of one of the functions bagging, boosting,
predict.bagging or predict.boosting. This is assumed to be the result of
some function that produces an object with two components named formula
and class, as those returned for instance by the bagging function.
newdata The same data frame used for building the object

Details
Intuitively, the margin for an observation is related to the certainty of its classification. It is cal-
culated as the difference between the support of the correct class and the maximum support of an
incorrect class

Value
An object of class margins, which is a list with only one component:

margins a vector with the margins.

Author(s)
Esteban Alfaro-Cortes <[email protected]>, Matias Gamez-Martinez <[email protected]>
and Noelia Garcia-Rubio <[email protected]>

References
Alfaro, E., Gamez, M. and Garcia, N. (2013): “adabag: An R Package for Classification with
Boosting and Bagging”. Journal of Statistical Software, Vol 54, 2, pp. 1–35.
Alfaro, E., Garcia, N., Gamez, M. and Elizondo, D. (2008): “Bankruptcy forecasting: An empirical
comparison of AdaBoost and neural networks”. Decision Support Systems, 45, pp. 110–122.
Schapire, R.E., Freund, Y., Bartlett, P. and Lee, W.S. (1998): “Boosting the margin: A new expla-
nation for the effectiveness of voting methods”. The Annals of Statistics, vol 26, 5, pp. 1651–1686.

See Also
bagging, boosting, plot.margins, predict.boosting, predict.bagging

Examples

#Iris example
library(rpart)
data(iris)
sub <- c(sample(1:50, 25), sample(51:100, 25), sample(101:150, 25))
iris.adaboost <- boosting(Species ~ ., data=iris[sub,], mfinal=3)
margins(iris.adaboost,iris[sub,])->iris.margins # training set
plot.margins(iris.margins)

# test set
plot.errorevol 25

iris.predboosting<- predict.boosting(iris.adaboost, newdata=iris[-sub,])

margins(iris.predboosting,iris[-sub,])->iris.predmargins
plot.margins(iris.predmargins,iris.margins)

#Examples with bagging

iris.bagging <- bagging(Species ~ ., data=iris[sub,], mfinal=3)
margins(iris.bagging,iris[sub,])->iris.bagging.margins # training set

iris.predbagging<- predict.bagging(iris.bagging, newdata=iris[-sub,])

margins(iris.predbagging,iris[-sub,])->iris.bagging.predmargins # test set
par(bg="lightyellow")
plot.margins(iris.bagging.predmargins,iris.bagging.margins)

plot.errorevol Plots the error evolution of the ensemble

Description
Plots the previously calculated error evolution of an AdaBoost.M1, AdaBoost-SAMME or Bagging
classifier for a data frame as the ensemble size grows

Usage
## S3 method for class 'errorevol'
plot(x, y = NULL, ...)

Arguments
x An object of class errorevol. This is assumed to be the result of some function
that produces an object with a component named error as that returned by the
errorevol function.
y This argument can be used to represent in the same plot the evolution of the test
and train errors, x and y, respectively. Should be NULL (by default) or an object
of class errorevol.
... further arguments passed to or from other methods.

Details
This can be useful to see how fast bagging or boosting reduce the error of the ensemble. in
addition, it can detect the presence of overfitting and, therefore, the convenience of pruning the
ensemble using predict.bagging or predict.boosting.

Value
A labeled plot is produced on the current graphics device (one being opened if needed).
26 plot.errorevol

Author(s)

Esteban Alfaro-Cortes <[email protected]>, Matias Gamez-Martinez <[email protected]>

and Noelia Garcia-Rubio <[email protected]>

References

Alfaro, E., Gamez, M. and Garcia, N. (2013): “adabag: An R Package for Classification with
Boosting and Bagging”. Journal of Statistical Software, Vol 54, 2, pp. 1–35.
Alfaro, E., Garcia, N., Gamez, M. and Elizondo, D. (2008): “Bankruptcy forecasting: An empirical
comparison of AdaBoost and neural networks”. Decision Support Systems, 45, pp. 110–122.
Breiman, L. (1996): “Bagging predictors”. Machine Learning, Vol 24, 2, pp.123–140.
Freund, Y. and Schapire, R.E. (1996): “Experiments with a new boosting algorithm”. In Pro-
ceedings of the Thirteenth International Conference on Machine Learning, pp. 148–156, Morgan
Kaufmann.
Zhu, J., Zou, H., Rosset, S. and Hastie, T. (2009): “Multi-class AdaBoost”. Statistics and Its
Interface, 2, pp. 349–360.

See Also

boosting, predict.boosting, bagging, predict.bagging, errorevol

Examples

data(iris)
train <- c(sample(1:50, 25), sample(51:100, 25), sample(101:150, 25))

cntrl<-rpart.control(maxdepth=1)
#increase mfinal in your own execution of this example to see
#the real usefulness of this function
iris.adaboost <- boosting(Species ~ ., data=iris[train,], mfinal=10, control=cntrl)

#Error evolution along the iterations in training set

errorevol(iris.adaboost,iris[train,])->evol.train
plot.errorevol(evol.train)

#comparing error evolution in training and test set

errorevol(iris.adaboost,iris[-train,])->evol.test
plot.errorevol(evol.test, evol.train)

# See the help of the functions error evolution and boosting

# for more examples of the use of the error evolution
plot.margins 27

plot.margins Plots the margins of the ensemble

Description
Plots the previously calculated margins of an AdaBoost.M1, AdaBoost-SAMME or Bagging clas-
sifier for a data frame

Usage
## S3 method for class 'margins'
plot(x, y = NULL, ...)

Arguments
x An object of class margins. This is assumed to be the result of some function
that produces an object with a component named margins as that returned by
the margins function.
y This argument can be used to represent in the same plot the margins in the test
and train sets, x and y, respectively. Should be NULL (by default) or an object of
class margins.
... further arguments passed to or from other methods.

Details
Intuitively, the margin for an observation is related to the certainty of its classification. It is cal-
culated as the difference between the support of the correct class and the maximum support of an
incorrect class

Value
A labeled plot is produced on the current graphics device (one being opened if needed).

Author(s)
Esteban Alfaro-Cortes <[email protected]>, Matias Gamez-Martinez <[email protected]>
and Noelia Garcia-Rubio <[email protected]>

References
Alfaro, E., Gamez, M. and Garcia, N. (2013): “adabag: An R Package for Classification with
Boosting and Bagging”. Journal of Statistical Software, Vol 54, 2, pp. 1–35.
Alfaro, E., Garcia, N., Gamez, M. and Elizondo, D. (2008): “Bankruptcy forecasting: An empirical
comparison of AdaBoost and neural networks”. Decision Support Systems, 45, pp. 110–122.
Schapire, R.E., Freund, Y., Bartlett, P. and Lee, W.S. (1998): “Boosting the margin: A new expla-
nation for the effectiveness of voting methods”. The Annals of Statistics, vol 26, 5, pp. 1651–1686.
28 predict.bagging

See Also
margins, boosting, predict.boosting, bagging, predict.bagging

Examples
library(mlbench)
data(BreastCancer)
l <- length(BreastCancer[,1])
sub <- sample(1:l,2*l/3)
cntrl <- rpart.control(maxdepth = 3, minsplit = 0, cp = -1)

BC.adaboost <- boosting(Class ~.,data=BreastCancer[sub,-1],mfinal=5, control=cntrl)

BC.adaboost.pred <- predict.boosting(BC.adaboost,newdata=BreastCancer[-sub,-1])

BC.margins<-margins(BC.adaboost,BreastCancer[sub,-1]) # training set

BC.predmargins<-margins(BC.adaboost.pred,BreastCancer[-sub,-1]) # test set
plot.margins(BC.predmargins,BC.margins)

predict.bagging Predicts from a fitted bagging object

Description
Classifies a dataframe using a fitted bagging object.

Usage
## S3 method for class 'bagging'
predict(object, newdata, newmfinal=length(object$trees), ...)

Arguments
object fitted model object of class bagging. This is assumed to be the result of some
function that produces an object with the same named components as that re-
turned by the bagging function.
newdata data frame containing the values at which predictions are required. The predic-
tors referred to in the right side of formula(object) must be present by name
in newdata.
newmfinal The number of trees of the bagging object to be used in the prediction. This
argument allows the user to prune the ensemble. By default all the trees in the
bagging object are used
... further arguments passed to or from other methods.
predict.bagging 29

Value
An object of class predict.bagging, which is a list with the following components:

formula the formula used.

votes a matrix describing, for each observation, the number of trees that assigned it to
each class.
prob a matrix describing, for each observation, the posterior probability or degree of
support of each class. These probabilities are calculated using the proportion of
votes in the final ensemble.
class the class predicted by the ensemble classifier.
confusion the confusion matrix which compares the real class with the predicted one.
error returns the average error.

Author(s)
Esteban Alfaro-Cortes <[email protected]>, Matias Gamez-Martinez <[email protected]>
and Noelia Garcia-Rubio <[email protected]>

References
Alfaro, E., Gamez, M. and Garcia, N. (2013): “adabag: An R Package for Classification with
Boosting and Bagging”. Journal of Statistical Software, Vol 54, 2, pp. 1–35.
Alfaro, E., Garcia, N., Gamez, M. and Elizondo, D. (2008): “Bankruptcy forecasting: An empirical
comparison of AdaBoost and neural networks”. Decision Support Systems, 45, pp. 110–122.
Breiman, L. (1996): "Bagging predictors". Machine Learning, Vol 24, 2, pp. 123–140.
Breiman, L. (1998). "Arcing classifiers". The Annals of Statistics, Vol 26, 3, pp. 801–849.

See Also
bagging, bagging.cv

Examples
#library(rpart)
#data(iris)
#sub <- c(sample(1:50, 25), sample(51:100, 25), sample(101:150, 25))
#iris.bagging <- bagging(Species ~ ., data=iris[sub,], mfinal=5)
#iris.predbagging<- predict.bagging(iris.bagging, newdata=iris[-sub,])
#iris.predbagging

## rpart and mlbench libraries should be loaded

library(rpart)
library(mlbench)
data(BreastCancer)
l <- length(BreastCancer[,1])
sub <- sample(1:l,2*l/3)
BC.bagging <- bagging(Class ~.,data=BreastCancer[,-1],mfinal=5,
control=rpart.control(maxdepth=3))
30 predict.boosting

BC.bagging.pred <- predict.bagging(BC.bagging,newdata=BreastCancer[-sub,-1])

BC.bagging.pred$prob
BC.bagging.pred$confusion
BC.bagging.pred$error

predict.boosting Predicts from a fitted boosting object

Description
Classifies a dataframe using a fitted boosting object.

Usage
## S3 method for class 'boosting'
predict(object, newdata, newmfinal=length(object$trees), ...)

Arguments
object fitted model object of class boosting. This is assumed to be the result of some
function that produces an object with the same named components as that re-
turned by the boosting function.
newdata data frame containing the values at which predictions are required. The predic-
tors referred to in the right side of formula(object) must be present by name
in newdata.
newmfinal The number of trees of the boosting object to be used in the prediction. This
argument allows the user to prune the ensemble. By default all the trees in
object are used
... further arguments passed to or from other methods.

Value
An object of class predict.boosting, which is a list with the following components:

formula the formula used.

votes a matrix describing, for each observation, the number of trees that assigned it to
each class, weighting each tree by its alpha coefficient.
prob a matrix describing, for each observation, the posterior probability or degree of
support of each class. These probabilities are calculated using the proportion of
votes in the final ensemble.
class the class predicted by the ensemble classifier.
confusion the confusion matrix which compares the real class with the predicted one.
error returns the average error.
predict.boosting 31

Author(s)
Esteban Alfaro-Cortes <[email protected]>, Matias Gamez-Martinez <[email protected]>
and Noelia Garcia-Rubio <[email protected]>

References
Alfaro, E., Gamez, M. and Garcia, N. (2013): “adabag: An R Package for Classification with
Boosting and Bagging”. Journal of Statistical Software, Vol 54, 2, pp. 1–35.
Alfaro, E., Garcia, N., Gamez, M. and Elizondo, D. (2008): “Bankruptcy forecasting: An empirical
comparison of AdaBoost and neural networks”. Decision Support Systems, 45, pp. 110–122.
Breiman, L. (1998): "Arcing classifiers". The Annals of Statistics, Vol 26, 3, pp. 801–849.
Freund, Y. and Schapire, R.E. (1996): "Experiments with a new boosting algorithm". En Pro-
ceedings of the Thirteenth International Conference on Machine Learning, pp. 148–156, Morgan
Kaufmann.
Zhu, J., Zou, H., Rosset, S. and Hastie, T. (2009): “Multi-class AdaBoost”. Statistics and Its
Interface, 2, pp. 349–360.

See Also
boosting, boosting.cv

Examples
## rpart library should be loaded
#This example has been hidden to fulfill execution time <5s
#library(rpart)
#data(iris)
#sub <- c(sample(1:50, 25), sample(51:100, 25), sample(101:150, 25))
#iris.adaboost <- boosting(Species ~ ., data=iris[sub,], mfinal=10)
#iris.predboosting<- predict.boosting(iris.adaboost, newdata=iris[-sub,])
#iris.predboosting$prob

## rpart and mlbench libraries should be loaded

## Comparing the test error of rpart and adaboost.M1
library(rpart)
library(mlbench)
data(BreastCancer)
l <- length(BreastCancer[,1])
sub <- sample(1:l,2*l/3)

BC.rpart <- rpart(Class~.,data=BreastCancer[sub,-1], maxdepth=3)

BC.rpart.pred <- predict(BC.rpart,newdata=BreastCancer[-sub,-1],type="class")
tb <-table(BC.rpart.pred,BreastCancer$Class[-sub])
error.rpart <- 1-(sum(diag(tb))/sum(tb))
tb
error.rpart

BC.adaboost <- boosting(Class ~.,data=BreastCancer[,-1],mfinal=10, coeflearn="Freund",

boos=FALSE , control=rpart.control(maxdepth=3))
32 prep_data

#Using the pruning option

BC.adaboost.pred <- predict.boosting(BC.adaboost,newdata=BreastCancer[-sub,-1], newmfinal=10)
BC.adaboost.pred$confusion
BC.adaboost.pred$error

prep_data Prepare Ranking Data for Item-Weighted Ensemble Algorithm

Description

The prep_data function prepares item-weighted ranking data for further analysis. It takes a ranking
matrix, predictors matrix, and weighting vector or matrix, and returns a data frame suitable for item-
weighted ensemble algorithms for rankings.

Usage

prep_data(y, x, iw)

Arguments

y an N by M matrix or data frame representing the ranking responses, where N is

the number of individuals and M is the number of items. Each row corresponds
to a ranking, ties are allowed.
x an N by K matrix or data frame containing the K predictors associated with each
individual ranking. Continuous variables are allowed, while the dummy coding
should be used for categorical variables.
iw a vector or matrix representing the item weights or dissimilarities for the ranking
data. For a vector, it should be a row vector of length M. For a matrix, it should
be a symmetric M by M matrix representing item dissimilarities.

Details

The prep_data function performs the following steps: Check the dimensions of the weighting
vector or matrix to ensure compatibility with the ranking data. Adjust the ranking matrix y using
the "min" method for ties. Convert the ranked matrix into a data frame. Generate the universe of
rankings using the ConsRank::univranks function. Match the ranking matrix y with the whole
universe of rankings to obtain a label for each ranking. Combine the Label column with the predictor
matrix. Remove rows with missing values. The function then returns the prepared data frame
for ensemble ranking. It also create the internal objects: item, perm_tab_complete_up, perm,
mat.dist that are employed in the Ensemble_ranking_IW function.
simulatedRankingData 33

Value
An N by (K+1) data frame containing the prepared item-weighted ranking data. The first column
"Label" contains the transformed ranking responses, and the remaining columns contain the predic-
tors.

References
Albano, A., Sciandra, M., and Plaia, A. (2023): "A Weighted Distance-Based Approach with
Boosted Decision Trees for Label Ranking." Expert Systems with Applications.
D’Ambrosio, A.[aut, cre], Amodio, S. [ctb], Mazzeo, G. [ctb], Albano, A. [ctb], Plaia, A. [ctb]
(2023). "ConsRank: Compute the Median Ranking(s) According to the Kemeny’s Axiomatic Ap-
proach. R package version 2.1.3", https://cran.r-project.org/package=ConsRank.
Plaia, A., Buscemi, S., Furnkranz, J., and Mencıa, E.L. (2021): "Comparing Boosting and Bagging
for Decision Trees of Rankings." Journal of Classification, pages 1–22.

Examples
# Prepare item-weighted ranking data
y <- matrix(c(1, 2, 3, 4, 2, 3, 1, 4, 4, 1, 3, 2, 2, 3, 1, 4), nrow = 4, ncol = 4, byrow = TRUE)
x <- matrix(c(0.5, 0.8, 1.2, 0.7, 1.1, 0.9, 0.6, 1.3, 0.4, 1.5, 0.7, 0.9), nrow = 4, ncol = 3)
iw <- c(2, 5, 5, 2)
dati <- prep_data(y, x, iw)

simulatedRankingData Simulated ranking data

Description
The simulatedRankingData dataset is a list that includes the following components:
The ranking matrix, y, contains the ranking matrix. It consists of 500 rows and 4 columns, indicating
the ranking positions. Each element in the matrix represents the rank assigned to an individual for
a particular item.
The predictor matrix x in the dataset consists of 20 continuous explanatory variables. These vari-
ables are used for predicting the rankings.

Usage
data(simulatedRankingData)

References
Albano, A., Sciandra, M., and Plaia, A. (2023): "A weighted distance-based approach with boosted
decision trees for label ranking." Expert Systems with Applications.
Index

∗ classif boosting, 4, 10, 13, 18, 21, 24, 26, 28, 31

adabag-package, 2 boosting.cv, 4, 11, 12, 31
autoprune, 5
bagging, 6 Ensemble_ranking_IW, 4, 14
bagging.cv, 8 errorevol, 4, 17, 26
boosting, 10 errorevol_ranking_vector_IW, 4, 18
boosting.cv, 12
errorevol, 17 importanceplot, 4, 20
importanceplot, 20
MarginOrderedPruning.Bagging, 4, 22
MarginOrderedPruning.Bagging, 22
margins, 4, 23, 28
margins, 23
plot.errorevol, 25 plot.errorevol, 4, 25
plot.margins, 27 plot.margins, 4, 24, 27
predict.bagging, 28 predict.bagging, 4, 7, 9, 18, 23, 24, 26, 28,
predict.boosting, 30 28
∗ datasets predict.boosting, 4, 11, 13, 18, 24, 26, 28,
simulatedRankingData, 33 30
∗ tree prep_data, 4, 32
adabag-package, 2
autoprune, 5 rpart, 5
bagging, 6
bagging.cv, 8 simulatedRankingData, 33
boosting, 10
boosting.cv, 12
errorevol, 17
importanceplot, 20
MarginOrderedPruning.Bagging, 22
margins, 23
plot.errorevol, 25
plot.margins, 27
predict.bagging, 28
predict.boosting, 30

adabag (adabag-package), 2
adabag-package, 2
adaboost.M1 (boosting), 10
autoprune, 4, 5

bagging, 4, 6, 9, 18, 21, 23, 24, 26, 28, 29

bagging.cv, 4, 7, 8, 29

34