Environmental monitoring and peat assessment using a multivariate

analysis of regional-scale geochemical data

McKinley, J., Grunsky, E., & Mueller, U. (2017). Environmental monitoring and peat assessment using a
multivariate analysis of regional-scale geochemical data. Mathematical Geosciences, 1-12. DOI:
10.1007/s11004-017-9686-x

Published in:
Mathematical Geosciences

Document Version:
Publisher's PDF, also known as Version of record

Queen's University Belfast - Research Portal:

Link to publication record in Queen's University Belfast Research Portal

Publisher rights
© The Author(s) 2017. This is an open access article published under a Creative Commons Attribution License
(https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium, provided the
author and source are cited.

General rights
Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other
copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated
with these rights.

Take down policy

The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to
ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws. If you discover content in the
Research Portal that you believe breaches copyright or violates any law, please contact [email protected].

Download date:11. Mar. 2018

Math Geosci
DOI 10.1007/s11004-017-9686-x

SPECIAL ISSUE

Environmental Monitoring and Peat Assessment Using

Multivariate Analysis of Regional-Scale Geochemical
Data

Jennifer M. McKinley1 · Eric Grunsky2 ·

Ute Mueller3

Received: 28 December 2016 / Accepted: 4 April 2017

© The Author(s) 2017. This article is an open access publication

Abstract A compositional multivariate approach was used to analyse regional-scale

soil geochemical data obtained as part of the Tellus Project generated by the Geological
Survey of Northern Ireland. The multi-element total concentration data presented
comprise X-ray fluorescence (XRF) analyses of 6862 rural soil samples collected at 20-
cm depth on a non-aligned grid at one site per 2 km2 . Censored data were imputed using
published detection limits. Each soil sample site was assigned to the regional geology
map, resulting in spatial data for one categorical variable and 35 continuous variables
comprised of individual and amalgamated elements. This paper examines the extent
to which soil geochemistry reflects the underlying geology or superficial deposits.
Since the soil geochemistry is compositional, log-ratios were computed to adequately
evaluate the data using multivariate statistical methods. Principal component analysis
(PCA) and minimum/maximum autocorrelation factors (MAF) were used to carry
out linear discriminant analysis (LDA) as a means to discover and validate processes
related to the geologic assemblages coded as age bracket. Peat cover was introduced as
an additional category to measure the ability to predict and monitor fragile ecosystems.
Overall prediction accuracies for the age bracket categories were 68.4 % using PCA
and 74.7 % using MAF. With inclusion of peat, the accuracy for LDA classification
decreased to 65.0 and 69.9 %, respectively. The increase in misclassification due to
the presence of peat may reflect degradation of peat-covered areas since the creation
of superficial deposit classification.

B Jennifer M. McKinley
[email protected]

1 School of Natural and Built Environment, Queen’s University Belfast, Belfast BT7 1NN, UK
2 Department of Earth and Environmental Sciences, University of Waterloo, Waterloo,
ON N2L 3G1, Canada
3 School of Science, Edith Cowan University, Joondalup, WA 6027, Australia

123
 Math Geosci

Keywords Compositional data analysis · Minimum/maximum autocorrelation

factors (MAF) · Linear discriminant analysis (LDA) · Log-ratios · Centred log-ratio
(clr) · Geochemistry

1 Introduction

A diversity of rock types observed across Northern Ireland represents three basement
terranes (Fig. 1a after Mitchell 2004). The Grampian Terrane and associated rocks in
the northwest have metamorphic igneous and sedimentary origins spanning the Pro-
terozoic Era. Psammites and semi-pelites are the dominant rock type, with subordinate
sandstones and conglomerates. The Midland Valley Terrane hosts Palaeozoic igneous
formations and Late Devonian–Early Carboniferous sedimentary rocks. Rock types
comprise red sandstones, limestone and mudstones with less common conglomerates.
The Southern Uplands–Down–Longford Terrane consists of granitic igneous intru-
sives and Lower Palaeozoic Ordovician and Silurian marine sedimentary rocks (lithic
arenites and sandstones). Palaeogene flood basalts and lava-derived sedimentary clays
cover a large portion of the Midland Valley and Grampian basement rocks in the north-
east of the country. The advance of ice sheets and their meltwaters over the last 100,000
years has left at least 80 % of the bedrock covered by superficial deposits, including
glacial till and post-glacial alluvium and peat (Fig. 1b). Monitoring peat coverage has
become important in calculating soil carbon stocks due to the relatively high carbon
density of peat and organic-rich soils. This is particularly important for Ireland (and
other Northern European countries), where some 16 % of the land surface is covered
by peat bog. In Northern Ireland, previous work has estimated the total amount of
carbon stored in vegetation to be 4.4 Mt compared with 386 Mt stored within soils
such as peat (Cruickshank et al. 1998).
A number of comprehensive regional and national soil sampling programmes have
been completed across the UK, including the British Geological Survey (BGS) G-
BASE survey and regional soil surveys for Northern Ireland (Jordan et al. 2001). These

Fig. 1 a Simplified geology of Northern Ireland (after Mitchell 2004); b map showing post-glacial peat-
covered areas

123
Math Geosci

have been used to assess baseline element concentrations in soils and normal back-
ground concentrations of contaminants (for example Ander et al. 2013). The Northern
Ireland Tellus Survey (GSNI 2007; Young and Donald 2013) included a ground-based
geochemical survey in which 6862 rural soil samples were collected between 1994
and 2006. Samples were collected on a grid of one sample site every 2 km2 , with
soils being collected at depths of 20 and 50 cm. The samples were analysed by X-ray
fluorescence spectrometry (XRFS) for 60 elements and inorganic compounds. Tellus
Survey field methods and analytical methodology are described in Smyth (2007) and
Young and Donald (2013). Soils and parent geology across Northern Ireland are typ-
ical for the geological and pedological conditions across the UK (Jordan et al. 2001)
as well as for several parts of Northern Europe, therefore the Tellus data set provides
the basis for a comprehensive study with relevancy not only for the whole of the UK,
but also Northern Europe. This paper explores the extent to which soil geochemistry
can be used to classify the underlying geology and moreover differentiate superficial
deposits such as peat.

2 Methods

Previous work by Grunsky et al. (2014) has demonstrated the effectiveness of apply-
ing log-ratio transforms, principal component analysis (PCA) and linear discriminant
analysis (LDA) to differentiate lithologies and glacial processes. This study involves
the use of both process discovery and validation methods within a compositional mul-
tivariate approach to analyse the rural Tellus soil data sampled at 20-cm depth. Many
geochemical data sets contain values that are reported at less than the lower limit
of detection, and these values are generally termed ‘censored’ (Grunsky 2010). For
this study, published detection limits (Young and Donald 2013) were used to impute
censored data; this resulted in 47 elements (Al, As, Ba, Bi, Br, Ca, Cd, Ce, Cl, Co,
Cr, Cs, Cu, Fe, Ga, Ge, Hf, I, K, La, Mg, Mn, Mo, Na, Nb, Nd, Ni, P, Pb, Rb, Sc,
Se, Si, Sm, Sn, Sr, Th, Ti, Tl, U, V, W, Y, Yb, Zn, Zr and total C) available for initial
analysis. Elements that occupy the same sites and/or substitute for other elements in
mineral structures can display collinearity when estimating statistical moments. In
many cases, the elements behave in identical ways and these elements can be summed
to a single variable without any loss of information or structure in the data. This is
often the case for rare-earth elements, and the degree of collinearity can be observed
in the loadings of the variables in a principal component biplot. An application of
clr-based PCA showed that several elements were near-collinear and prompted an
amalgamation of the data based on the following proxies: light rare-earth elements
(LREE), La, Ce, Nd along with Th; heavy rare-earth elements (HREE), Yb and Hf;
elements associated with mafic minerals (Mafic), Fe, V, Cr and Sc; alkali elements
associated with feldspars (Ba_Na_K_Rb), Ba, Na, K and Rb; and lastly elements asso-
ciated with a feldspar silicate framework (Al_Ga), Al and Ga. This reduced the total
number of elements and amalgamated elements to 35, and these were the basis of all
further analysis.
Each soil sample site was assigned to the regional geology map and then age
brackets provided by Geological Survey Northern Ireland (GSNI) using the dominant

123
 Math Geosci

Fig. 2 Map showing samples tagged with age bracket classification. Full age bracket classes are provided
in Table 1

age bracket for the map polygon (Fig. 2; Table 1). A process discovery approach
(Grunsky 2010) involves use of unsupervised multivariate methods such as principal
component analysis (PCA). An essential part of the process discovery phase is a
suitable choice of transform to overcome the problem of closure. Therefore, to account
for the requirements of compositional data analysis and avoid closure issues, the
geochemical data were transformed using centred log-ratios (clr, Aitchison 1986).
Analysis of variance (ANOVA) is a commonly used method for determining the
statistical distinctiveness of groups based on the observations and variables (Grunsky
and Kjarsgaard 2016). The results will determine whether or not there is sufficient
statistical separation of the groups to undertake a classification such as linear dis-
criminant analysis (LDA, Venables and Ripley 2002). Garrett (1989) suggests that the
ratio of observations to the total number of variables and groups should be a minimum
of 3:1 and ideally greater than 10:1 (Garrett 1989). To ensure that this requirement
is fulfilled, data compression was applied. Two potential compression methods are
the use of principal components and minimum/maximum autocorrelation (MAF) fac-
tors. The use of principal components to represent the variables is well established.
However, in this approach, spatial relationships between the variables are ignored.
One way to address this failure is to use minimum/maximum autocorrelation factors
instead (Mueller and Grunsky 2016). These are derived from the given data by first
performing a principal component analysis and then a rotation based on the spectral

123
Math Geosci

Table 1 Geological age bracket classification

Code Number of tagged Geological age bracket

Tellus samples

CzOl 151 Cenozoic, Palaeogene, Oligocene

CzPl 1671 Cenozoic, Palaeogene, Palaeocene
Mes 330 Mesozoic, Cretaceous, Jurassic, Triassic
NeoP 978 Neoproterozoic, Dalradian Supergroup
Pg 93 Palaeogene
Pl 146 Palaeozoic, Lower–Middle Ordovician, Lower Palaeozoic
PlCr 1526 Palaeozoic, Carboniferous, Mississippian, Pennsylvanian
PlDv 296 Palaeozoic, Upper Devonian–Carboniferous, Lower Devonian, Middle
Devonian, Devonian
PlOr 1289 Palaeozoic, Middle–Upper Ordovician, Ordovician–Silurian, Permian, Silurian
PlSi 163 Caledonian (Silurian–Devonian)

decomposition of a variance–covariance matrix of the PCA-transformed and scaled

data at a lag (h), typically chosen to represent the sample spacing (Desbarats and
Dimitrakopoulos 2000). The MAF transformation can also be seen as the solution
of a generalised eigenvalue problem (Bandarian and Mueller 2008), and this is the
approach taken here. For both PCA and MAF, the decision on the number of factors
to use to represent the data is determined experimentally based on the behaviour of
the F-values in the ANOVA.
Following the data compression step, n-fold cross-validation LDA can be used
to derive posterior probabilities of class membership. Since these probabilities
are compositional (van den Boogaart and Tolosana-Delgado 2006; Egozcue and
Pawlowsky-Glahn 2016), an appropriate transformation is required prior to their
interpolation in order to ensure that estimates are non-negative and adhere to the
constant sum constraint. In this study, ordinary co-kriging was applied to the isomet-
ric log-ratio (ilr)-scores of the posterior probabilities, and this step was followed by
back-transformation to interpolated probabilities.

3 Results and Discussion

Based on the geological age bracket classification, without peat, PCA showed that
72 % of the variation was determined by the first four principal components (PCs),
implying ‘significant’ structure in the data. Analysis of variance showed that only 10
PCs were necessary to classify the soil geochemical data. To consider an improvement
over PCA that uses the spatial relationships of the data, a classification based on MAF
analysis was undertaken using the first eight dominant factors (Fig. 3a). Twenty-fold
cross-validation LDA, using PCA and MAF, resulted in overall classification accuracy
of 68.4 % (PCA) and 74.7 % (MAF) for the geological age bracket classification.
More specifically, except for PlDv and PlOr, the use of MAF and cross-validation
LDA resulted in improvements in both recall (quotient of total number of correctly

123
 Math Geosci

Fig. 3 ANOVA for soil geochemistry age bracket classification using PCA and MAF analysis: a without
peat and b including peat in the classification

classified sites and total number of sites in the class) and precision (quotient of total
number of correctly classified sites and total number of sites allocated to the class),
particularly so for the classes with low number of sites (Table 2; Fig. 4).
The mapped posterior probabilities for six of the age bracket classes (CzPl, NeoP,
PlCr, PlDv, PlOr and PlSi) are shown in Fig. 5. In the case of the CzPl and PlSi age
brackets (Fig. 5a, f), the locations of non-zero probability are quite well constrained and
the probabilities of occurrence are generally very high. The Palaeocene Antrim Lava
Group, within the CzPl age bracket class, dominates the landscape of the North West of
Ireland comprising the largest remnant of the North Atlantic Igneous Province (Cooper

123
Math Geosci

Table 2 Recall and precision for classification results based on PCA and MAF

Code Number of PCA MAF

sites

% Classified Precision Recall % Classified Precision Recall

correctly correctly

CzOl 151 3.97 0.38 0.04 13.91 0.51 0.14

CzPl 1671 86.12 0.91 0.86 87.07 0.92 0.87
Mes 330 8.18 0.25 0.08 36.06 0.33 0.36
NeoP 978 66.36 0.61 0.66 83.64 0.71 0.84
Pg 93 69.89 0.71 0.7 73.12 0.73 0.73
Pl 146 0.00 0 0 9.59 0.3 0.1
PlCr 1526 71.76 0.56 0.72 70.38 0.7 0.7
PlDv 296 7.09 0.54 0.07 28.38 0.52 0.28
PlOr 1289 85.10 0.7 0.85 90.15 0.78 0.9
PlSi 163 90.18 0.69 0.9 90.18 0.84 0.9

Fig. 4 Linear discriminant analysis (LDA) using MAF analysis for soil geochemistry age bracket classi-
fication (without peat) using the first eight dominant factors. Colour shows the predicted class, while the
symbol shows the actual class

and Mitchell 2013). Petrographical studies demonstrate the consistent geochemical

signature of the fine-grained, olivine basalt lava formations. This helps to explain the
well-constrained and high probabilities of occurrence for this age bracket. Likewise the
PlSi class (Fig. 5f) closely constitutes the Caledonian granodiorite igneous complex. In
contrast, the PlDv class (Fig. 5d), which is also quite well constrained, has much lower
probabilities of occurrence. This class, which has 296 tagged samples, represents a
broad range of Palaeozoic rocks representing a fault-bounded non-marine sedimentary
basin sequence of interbedded sandstones, mudstones and conglomerates. The spatial
maps of co-kriging estimates of the posterior probabilities, shown for the same age

123
 Math Geosci

Fig. 5 Posterior probabilities for age bracket classes a CzPl, b NeoP, c PlCr, d PlDv, e PlOr and f PlSi.
Geological age bracket classes provided in full in Table 1

bracket classifications (Fig. 6), consolidate the findings from the mapped posterior
probabilities (Fig. 5).

3.1 Peat Assessment

Since the aim of this study is to elucidate the relationship between soil geochemistry
and post-glacial deposits for environmental monitoring, the next stage of the analysis
explored whether peat cover could be predicted from the classification. For this, the
geological age bracket designation was adapted to include the presence of peat based
on GSNI superficial deposit polygons (Fig. 1b) and linear discriminant analysis (LDA)
undertaken. As was the case for the classification based on the age brackets only, 10
PCA factors and 8 MAF factors were sufficient for the classification via LDA (Fig. 3b).

123
Math Geosci

Fig. 6 Spatial maps of co-kriging estimates of the posterior probabilities for a CzPl, b NeoP, c PlCr, d
PlDv, e PlOr and f PlSi. Geological age bracket classes provided in full in Table 1

Using LDA, the presence of peat was clearly differentiated from the other classifica-
tions (Fig. 7). The classification accuracies for the age bracket classes, including peat,
were 65.0 % (PCA) and 69.9 % (MAF). The prediction accuracies for both data types
are lower than for those where peat was not included as a class. The presence of peat
results in more classification confusion, most likely because the peat composition
retains geochemical characteristics of the underlying lithology and the organic com-
position of the peat itself. The plotted MAF posterior probabilities (Fig. 8) demonstrate
a good match between the reported peat areas (Fig. 1b) and the highest probability for
peat. However, there are areas of mapped peat where the estimated probabilities of
occurrence of peat are low. The explanation for this misclassification of peat may be
twofold: these areas may indicate degradation of peat-covered areas since the creation
of the superficial deposit classification, or a further refinement in the classification of
peat is required. Irish peatland is divided into blanket peatland (approximately 85 %)

123
 Math Geosci

Fig. 7 Linear discriminant analysis (LDA) including the presence of peat (shown as green symbols) using
MAF analysis. Colour shows the predicted class, while symbols show the actual class

Fig. 8 Plotted MAF posterior probabilities overlain on areas of reported peat

and raised peat bogs (approximately 15 %; Tomlinson and Davidson 2000). Blanket
bogs typically form on gentle slopes within upland regions [>315 m above sea level
(SL); Hamilton 1982]. The distribution of blanket bogs is more spatially continuous
and associated with areas of high precipitation (rainfall exceeding 1200 mm). Raised
bogs develop primarily in lowland areas (<200 m above SL; Wheeler and Shaw 1995)
where accumulating peat in fens becomes isolated from the groundwater supply. This
process of accumulation gradually forms a dome of ombrogenous peat above the fen,

123
Math Geosci

giving raised bogs a distinct topography, with steep margins to the main bog expanse.
Raised bogs are more limited in extent and occur as isolated features. Prediction of
peat-covered areas using MAF analysis methods, which use the spatial relationships
of the data, has been more successful in predicting the more extensive upland blanket
bogs than lowland raised bogs.

4 Conclusions

Compositional multivariate techniques, PCA and MAF analysis methods were used
to determine the influence of underlying geology on the soil geochemistry signature.
The approach was explored for environmental monitoring of peat to ascertain whether
peat cover could be predicted from the classification. Using LDA, the presence of
peat was clearly differentiated from the other lithological classifications. Moreover,
the prediction accuracy for LDA classification improved using MAF analysis. In an
attempt to reduce the number of areas of misclassification of peat, further work will
examine the influence of underlying lithologies on elemental concentrations in peat
composition and the effect of this in classification analysis.

Acknowledgements The Tellus Project was carried out by GSNI and funded by The Department for
Enterprise, Trade and Investment (DETINI) and The Rural Development Programme through the Northern
Ireland Programme for Building Sustainable Prosperity.

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 Interna-
tional License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution,
and reproduction in any medium, provided you give appropriate credit to the original author(s) and the
source, provide a link to the Creative Commons license, and indicate if changes were made.

References
Aitchison J (1986) The statistical analysis of compositional data. Chapman and Hall, New York
Ander EL, Johnson CC, Cave MR, Palumbo-Roe B, Nathanail CP, Lark RM (2013) Methodology for the
determination of normal background concentrations of contaminants in English soil. Sci Total Environ
454–455:604–618. doi:10.1016/j.scitotenv.2013.03.005
Bandarian EM, Mueller UA (2008) Reformulation of direct minimum/maximum autocorrelation factors as
a generalised Eigenvalue problem. In: Ortiz JM, Emery X (eds) Geostats 2008, vol 2. Universidad De
Chile, Santiago, Chile, pp 1173–1178
Cooper M, Mitchell W (2013) Geology. In: Young ME, Donald AE (eds) A guide to the tellus data 2013.
Geological Survey of Northern Ireland, Belfast, pp 5–20
Cruickshank MM, Tomlinson RW, Devine PM, Milne R (1998) Carbon in the vegetation and soils of
Northern Ireland. Biol Environ Proc R Ir Acad 98B(1):9–21
Desbarats AJ, Dimitrakopoulos R (2000) Geostatistical simulation of regionalized pore-size distributions
using min/max autocorrelation factors. Math. Geol. 23(8):919–941
Egozcue JJ, Pawlowsky-Glahn V (2016) Changing the reference measure in the simplex and its weighting
effects. Austrian J Stat 45:25–44. doi:10.17713/ajs.v45i4.126
Garrett RG (1989) A robust multivariate allocation procedure with applications to geochemical data. In:
Agterberg F, Bonham-Carter GF (eds) Statistical applications in earth sciences, geological survey
paper 89-9: 309–318
Geological Survey Northern Ireland (GSNI) (2007) Tellus project overview. https://www.bgs.ac.uk/gsni/
Tellus/index.html. Accessed 7 Mar 2017

123
 Math Geosci

Grunsky EC, Kjarsgaard BA (2016) Recognizing and validating structural processes in geochemical data.
In: Martin-Fernandez JA, Thio-Henestrosa S (eds) Compositional data analysis, vol 187. Springer
proceedings in mathematics and statistics, pp 85–116, 209 pp. doi:10.1007/978-3-319-44811-4_7
Grunsky EC, Mueller UA, Corrigan D (2014) A study of the lake sediment geochemistry of the Melville
Peninsula using multivariate methods: applications for predictive geological mapping. J Geochem
Explorn 141:15–41. doi:10.1016/j.gexplo.2013.07.013
Grunsky EC (2010) The interpretation of geochemical survey data. Geochem Explor Environ Anal 10(1):27–
74
Hamilton AC (1982) Peatland. In: Cruickshank JG, Wilcock DN (eds) Northern Ireland environment and
natural resources. QUB, Belfast, pp 185–206
Jordan C, Higgins A, Hamill K, Cruickshank JG (2001) The soil geochemical atlas of Northern Ireland.
Department of Agriculture and Rural Development, NI
Mitchell W (2004) The geology of Northern Ireland: our natural foundation. Geological Survey of Northern
Ireland, Belfast
Mueller UA, Grunsky EC (2016) Multivariate spatial analysis of lake sediment geochemical data. Melville
Peninsula, Nunavut, Canada. Appl Geochem 75:247–262. doi:10.1016/j.apgeochem.2016.02.007
Smyth D (2007) Methods used in the Tellus geochemical mapping of Northern Ireland. British geological
survey open report or/07/022
Tomlinson RW, Davidson L (2000) Estimates of carbon stores in four Northern Irish lowland raised bogs.
Suo 51:169–179
van den Boogaart KG, Tolosana-Delgado R (2006) Compositional data analysis with the R. In: Buccianti A,
Mateu-Figueras G, Pawlowsky-Glahn V (eds) Compositional data analysis: from theory to practice.
The Geological Society, London
Venables WN, Ripley BD (2002) Modern applied statistics with S. Springer. ISBN 0-387-95457-0
Wheeler BD, Shaw SC (1995) Restoration of damaged peatlands. HMSO, London
Young ME, Donald AE (2013) A guide to the Tellus data. Geological Survey of Northern Ireland, Belfast

123