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 Ecological Indicators 52 (2015) 394–403

Contents lists available at ScienceDirect

Ecological Indicators
journal homepage: www.elsevier.com/locate/ecolind

A comparative assessment of support vector regression, artificial

neural networks, and random forests for predicting and mapping soil
organic carbon stocks across an Afromontane landscape
Kennedy Were a,b,∗ , Dieu Tien Bui c , Øystein B. Dick a , Bal Ram Singh d
a
Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway
b
Kenya Agricultural Research Institute, Kenya Soil Survey, P.O. Box 14733-00800, Nairobi, Kenya
c
Department of Economics and Computer Sciences, Faculty of Arts and Sciences, Telemark University College, NO-3800 Bø, Norway
d
Department of Environmental Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway

a r t i c l e i n f o a b s t r a c t

Article history: Soil organic carbon (SOC) is a key indicator of ecosystem health, with a great potential to affect climate
Received 28 June 2014 change. This study aimed to develop, evaluate, and compare the performance of support vector regres-
Received in revised form sion (SVR), artificial neural network (ANN), and random forest (RF) models in predicting and mapping
29 November 2014
SOC stocks in the Eastern Mau Forest Reserve, Kenya. Auxiliary data, including soil sampling, climatic,
Accepted 24 December 2014
topographic, and remotely-sensed data were used for model calibration. The calibrated models were
applied to create prediction maps of SOC stocks that were validated using independent testing data.
Keywords:
The results showed that the models overestimated SOC stocks. Random forest model with a mean error
Random forests
Artificial neural networks
(ME) of −6.5 Mg C ha−1 had the highest tendency for overestimation, while SVR model with an ME of
Support vector regression −4.4 Mg C ha−1 had the lowest tendency. Support vector regression model also had the lowest root mean
Soil organic carbon squared error (RMSE) and the highest R2 values (14.9 Mg C ha−1 and 0.6, respectively); hence, it was the
Digital soil mapping best method to predict SOC stocks. Artificial neural network predictions followed closely with RMSE, ME,
Eastern Mau and R2 values of 15.5, −4.7, and 0.6, respectively. The three prediction maps broadly depicted similar
Kenya spatial patterns of SOC stocks, with an increasing gradient of SOC stocks from east to west. The highest
stocks were on the forest-dominated western and north-western parts, while the lowest stocks were on
the cropland-dominated eastern part. The most important variable for explaining the observed spatial
patterns of SOC stocks was total nitrogen concentration. Based on the close performance of SVR and ANN
models, we proposed that both models should be calibrated, and then the best result applied for spatial
prediction of target soil properties in other contexts.
© 2014 Elsevier Ltd. All rights reserved.

1. Introduction food security, and sustainable development. Soil organic carbon

Soils sustain life on Earth by delivering various ecosystem ser-
vices. For example, they are essential for producing food, fibre, fuel,
and raw materials, as well as for maintaining the climatic and ter-
restrial systems (Chen et al., 2002). The rapid land use-land cover
changes (LULCC), especially conversion of natural ecosystems to
agro-ecosystems, is straining the world’s soils. Agricultural land
uses modify the soil’s physical, chemical, and biological properties
leading to soil degradation, particularly depletion of soil organic
matter (SOM). This in turn has implications for global climate,
∗ Corresponding author at: Department of Mathematical Sciences and Technology,
Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway.
Tel.: +47 966 563 62; fax: +47 649 654 01.
E-mail address: kenwerez@yahoo.com (K. Were).
(SOC), which is the major constituent of SOM, determines the soil’s
physical, chemical, and biological properties. It maintains soil qual-
ity by supplying nutrients, enhancing cation exchange capacity,
supporting biodiversity, and improving aggregation and water-
holding capacity (Bationo et al., 2007). Depletion of SOM occurs
because of frequent tillage and other disturbances, which disinte-
grate the aggregates and alter aeration, moisture, and temperature
conditions in the soil. This accelerates microbial decomposition
and oxidation of SOM to CO2 , which increases the atmospheric
concentrations of CO2 and global warming (Murty et al., 2002;
Batlle-Aguilar et al., 2011; Wiesmeier et al., 2012). The threat of
global warming is disturbing because the world’s soils contain
about 1500 Pg C (1 Pg = 1015 g) to 1 m-depth, which is twice the
amount of C in the atmospheric pool (750 Pg C), and almost three
times in the biotic pool (610 Pg C) (Lal, 2004; Smith, 2004, 2008).
Thus, even slight changes in SOC pool can significantly impact on

http://dx.doi.org/10.1016/j.ecolind.2014.12.028
1470-160X/© 2014 Elsevier Ltd. All rights reserved.
 K. Were et al. / Ecological Indicators 52 (2015) 394–403
the global C cycle, climate, and soil properties (Powlson et al., 2011).
In the face of climate change and food insecurity, scientists have
focused their attention on LULCC and SOC storage research. There
is consensus that sustainable use of soil resources is one of the ways
to manage climate change and food insecurity issues. This requires
a deeper understanding of the spatial distribution of SOC storage
to guide policy formulation.
Consequently, many tools have been developed and tested
to help scientists analyze soil processes, and derive spatially-
continuous information on soil properties at different scales. The
open accessibility to most geographic information systems (GIS)
and remotely-sensed data and technologies has boosted these
efforts. This forms the basis of digital soil mapping (DSM). In DSM,
the variability of a target soil property is explained by its relation-
ships with soil-forming factors, such as topography, climate, land
use, vegetation, and soil type. This is underpinned by Jenny’s (1941)
seminal work, which considered soil development as a function of
climate (c), organisms (o), relief (r), parent material (p), and time
(a). This function was later expanded by McBratney et al. (2003) to
include soil properties (s) and space (n) under the famous SCORPAN
framework. Numerous statistical techniques have been applied in
digital mapping of SOC stocks, including multiple linear regression
(Meersmans et al., 2008), partial least square regression (Amare
et al., 2013), generalized linear models (Yang et al., 2008), lin-
ear mixed models (Doetterl et al., 2013; Karunaratne et al., 2014),
geographically-weighted regression (Mishra et al., 2010; Kumar
et al., 2013), kriging (Cambule et al., 2014), and regression-kriging
(Hengl et al., 2004, 2007; Kumar et al., 2012). Recently, a few studies
also applied new methods from the machine learning field, such as
artificial neural networks (Malone et al., 2009; Jaber and Al-Qinna,
2011; Li et al., 2013), support vector machines (Rossel and Behrens,
2010), boosted regression trees (Martin et al., 2011), and random
forests (Grimm et al., 2008; Wiesmeier et al., 2011; Vågen and
Winowiecki, 2013; Vågen et al., 2013) to map SOC stocks. Machine
learning methods overcome the shortcomings of parametric and
non-parametric statistical methods, such as spatial autocorrelation,
non-linearity, and overfitting (Drake et al., 2006). This improves the
prediction accuracy of spatial models. Despite the merits, applica-
tion of machine learning techniques in DSM is still rare (Vågen et al.,
2013).
Therefore, in this study, we aimed to develop, evaluate, and
compare the performance of random forests (RF), support vector
machines for regression (SVR), and artificial neural networks (ANN)
models in predicting and mapping the variability of SOC stocks in
the Eastern Mau Forest Reserve, Kenya. The distinction between
this study and the previous ones is that SVR with the recently
proposed sequential minimal optimization (SMO) algorithm (Platt,
1999; Smola and Schölkopf, 2004) was implemented. This relatively
new algorithm has been valuable for diverse environmental appli-
cations, but seldom used to model and map SOC stocks and other
soil properties.
2. Materials and methods
2.1. Study area
The study was conducted in the Eastern Mau Forest Reserve
(∼650 km2 ), which is bounded by the latitudes 0◦ 15 –0◦ 40 S and
the longitudes 35◦ 40 –36◦ 10 E (Fig. 1). It is part of the largest
closed-canopy Afromontane forest in Eastern Africa, and provides
essential ecosystem services. This is despite the deforestation and
degradation experienced since the mid-1990s because of illegal
logging, charcoal burning, and encroachments, as well as excision
of ∼61,023 ha for human settlement (Government of Kenya, 2009;
UNEP, 2009). The climate is cool and humid thanks to the high
395
altitudes ranging between 2210 and 3070 m above sea level. The
mean annual rainfall varies between 935 and 1287 mm, while the
mean annual temperatures range from 9.8 to 17.5 ◦ C (Jaetzold et al.,
2010). The Njoro, Naishi, and Larmudiac Rivers drain the eastern
slopes into Lake Nakuru, while the Nessuiet flow northwards into
Lake Bogoria, and the Rongai River into Lake Baringo. The physiog-
raphy and lithology consists of major scarps and uplands covered
with pyroclastic rocks (i.e., pumice tuffs) of tertiary-quaternary vol-
canic age. The rocks decompose into deep to very deep, dark reddish
brown clayey, friable and smeary soil aggregates with humic top-
soils: the resultant soils are classified as Mollic Andosols (McCall,
1967; Jaetzold et al., 2010). The major land uses are forestry, agri-
culture, and grazing. The red stinkwood (Prunus Africana), bamboo
(Arundinaria alpina), red cedar (Juniperus procera), African wild
olive (Olea europaea ssp. Africana), East African olive (Olea capensis
ssp. hochstetteri), broad-leaved yellowwood (Podocarpus latifolius),
brittlewood (Nuxia congesta), clematis (Clematis hirsuta), schefflera
(Schefflera volkensii), and forest dombeya (Dombeya torrida) are
dominant in the indigenous forests, and pine (Pinus patula) and
cypress (Cupressus lusitanica) in the plantation forests. The major
crops grown are maize (Zea mays), beans (Phaseolus vulgaris), wheat
(Triticum aestivum), and potatoes (Solanum tuberosum).
2.2. Soil data
2.2.1. Sampling design and soil sampling
We conducted field campaign from June to August 2012. Before
that, sampling points were generated randomly in a GIS with agro-
ecological zones as the stratifying factor, and then a map showing
the distribution of the points was produced for field use. In the
field, plots measuring 30 × 30 m were laid out at each sampling
point and soil samples collected at 0–15 cm and 15–30 cm depths
from the centres and corners of these plots using an auger. Sam-
ples taken from similar depths in a plot were properly mixed and
bulked into one composite sample weighing about 500 g. For bulk
density (BD) determination, a core ring sampler (5 cm in diameter,
5 cm in height) was used to collect undisturbed samples from each
depth at the centre of each plot. Three hundred and twenty (320)
soil samples were collected from 160 sampling plots for chemical
and physical analysis, and a similar number for BD determination.
Supplementary soil data that had been collected similarly from 60
other sampling plots for LULCC impact assessment (Were et al.,
2015) were also used. Thus, soil data from 220 sampling plots were
used for spatial modelling.
2.2.2. Determination of soil properties
The collected soil samples were air-dried, ground, and passed
through a 2 mm mesh at the National Agricultural Research Lab-
oratories. The Walkley-Black wet oxidation method (Nelson and
Sommers, 1982) and Kjeldahl digestion method (Bremner and
Mulvaney, 1982) were used to determine SOC concentrations and
TN concentrations, respectively. The hydrometer method (Day,
1965) was used to analyze particle size distribution, the core
method (Blake, 1965) to determine BD, and the Mehlich method
(Okalebo et al., 2002) to estimate phosphorous (P) content. A
flame-photometer was used to measure potassium (K) content, an
atomic absorption spectrophotometer to measure calcium (Ca) and
magnesium (Mg) contents, and a pH metre to measure pH (1:2.5
soil-water) (Okalebo et al., 2002).
2.2.3. Estimation of SOC stocks
The SOC stocks, i.e., mass of C per unit area for a given depth,
were calculated according to Eq. (1) (Aynekulu et al., 2011):
SOC
SOCst = × BD × D × 100 (1)
100
396 K. Were et al. / Ecological Indicators 52 (2015) 394–403
Fig. 1. Geographical location of the study area.
where SOCst is the soil organic carbon stock (Mg C ha−1 ), SOC is the
soil organic carbon concentration (%, which is then converted to g
C g−1 soil), BD is the bulk density (g cm−3 ), D is the depth (cm), and
100 is the multiplication factor to convert the SOC per unit area
from g C cm2 to Mg C ha−1 . Coarse particles were negligible due to
the softness of the volcanic rocks; hence, Eq. (1) does not account for
them. The SOC stocks in the surface (0–15 cm) and subsurface soils
(15–30 cm) were summed up to obtain the total stocks to 30 cm
depth.
2.3. Environmental data
Based on the SCORPAN conceptual model of soil development
(McBratney et al., 2003) and review of literature (e.g., Liu et al.,
2006; Vasques et al., 2010; Kumar and Lal, 2011; Kumar et al., 2012;
Li et al., 2013; Shelukindo et al., 2014), we selected a priori nine-
teen (19) environmental variables (predictors) with the potential
to explain the spatial variability of SOC stocks, and retrieved them
from existing spatial databases. Climate data (temperature and
rainfall) were obtained from www.worldclim.org, land cover data
from Were et al. (2013), elevation data (digital elevation model;
DEM) from http://srtm.csi.cgiar.org/, and Landsat 8 Operational
Land Imager (OLI) data from http://earthexplorer.usgs.gov/. Four
terrain parameters, including slope, curvature, aspect, and topo-
graphic wetness index (TWI) were extracted from the DEM (Wilson
and Gallant, 2000). Normalized Difference Vegetation Index (NDVI)
was derived from OLI band 4 (red) and 5 (near infra-red) after con-
version of the digital numbers to top-of-atmosphere reflectance.
The first component (PC1) from principal component analysis of
OLI band 2, 3, 4, 5, 6, and 7 was also included. The data, all of which
were in raster format, were transformed to UTM WGS84 Zone 36S
and subsets made. The climatic grids were resampled from 1 km
to 30 m using the nearest neighbour method, to match them with
the other raster grids. As in Kumar and Lal (2011), soil data from
the laboratory, including sand content, silt content, clay content,
Ca, Mg, P, K, TN, and pH were also integrated into the GIS database
both as points in vector format and as raster grids after interpo-
lation by ordinary kriging. Ordinary kriging has been widely used
to optimize the prediction of soil properties at unsampled loca-
tions in pedological studies (Chaplot et al., 2010; Pachomphon et al.,
2010; Tesfahunegn et al., 2011; Marchetti et al., 2012; Elbasiouny
et al., 2014). Finally, the attribute values of all the other raster grids
(e.g., slope, rainfall, and temperature) were extracted to the points,
which were the main input for spatial modelling.
3. Spatial modelling and prediction
3.1. Exploratory data analysis
We first estimated the descriptive statistics of the target vari-
able, followed by pairwise Pearson’s product-moment correlation
analysis to detect collinearity between the predictors, as well as
their correlation with the target variable. Predictors that were
highly correlated (r ≥ 0.8), and had high variance inflation factors
(VIFs ≥ 10) in regression analysis were excluded from modelling.
 K. Were et al. / Ecological Indicators 52 (2015) 394–403 397

3.2. Model training that minimized the empirical risk (Eq. (3)) (Pozdnoukhov, 2005;
Ruß and Kruse, 2010):
After exploring the data (n = 220), we randomly split it into train-
1
N
ing (n = 176) and testing (n = 44) sets. The former was used to model
Remp = Lε (y − f (x)) (3)
the relationships between the site-specific SOC stocks and the pre- N
i=1
dictors, and the latter to evaluate the predictive performance of
the models developed. For modelling purpose, RF, SVR, and ANN where Lε is the loss function, which penalizes the model in case
algorithms were used. of differences between the training data and model predictions
(i.e., errors). An ε-insensitive loss function was used (Eq. (4)) where
3.2.1. Random forests smaller errors than the specified non-negative constant ε were not
The algorithm is an extension of bagging (i.e., bootstrap aggre- penalized (Gunn, 1998; Pozdnoukhov, 2005).
  
gation) and a competitor to boosting (Cutler et al., 2012). It uses 0 for y − f (x) < ε
Lε (y − f (x)) =   (4)
either categorical (i.e., classification) or continuous (i.e., regression) y − f (x) − ε otherwise
response variables, and either categorical or continuous predic-
tor variables. As described by Cutler et al. (2012), the algorithm Prior to developing the SVR function f(x), the quadratic program-
worked by growing an ensemble of regression trees based on binary ming optimization problem shown in Eq. (5) was solved using the
recursive partitioning, where the predictor space at each tree node SMO algorithm (Platt, 1999; Smola and Schölkopf, 2004).
was partitioned based on binary splits on a subset of randomly
1 
N N
selected predictors. At each binary split, the response data were
max ˛, ˛∗ − (˛i − ˛∗i )(˛j − ˛∗j )K(xi , xj )
grouped into two descendant nodes to maximize homogeneity, 2
i=1 j=1
and the best binary split was selected. The response data for each
tree were obtained through bootstrap sampling (with replacement) 
N

N
of original observations in the training set. Each descendant node −ε (˛i + ˛∗i ) + yi (˛i + ˛∗i ) (5)
of the selected split was treated similarly as the original (root) i=1 i=1
node, and the process continued recursively until a stopping cri-
terion was met at a terminal node. The trees were grown to their with the constraints given in Eq. (6):
⎧ N
⎨ (˛ + ˛∗ ) = 0
maximum sizes with the results being combined by unweighted
⎪
averaging to make predictions. In RF modelling, the training param- i i
eters that needed specification were: (i) the number of trees to grow (6)
⎪
⎩ i=1
in the forest (ntree ), (ii) the number of randomly selected predictor 0≤ ˛i , ˛∗j ≤C for i = 1, . . .N
variables at each node (mtry ), and (iii) the minimal number of obser-
vations at the terminal nodes of the trees (nodesize). These were where ˛j and ˛∗jare the weights (Lagrange multipliers), which
set to 1000, 12, and 5, respectively. The default of ntree was 500, but determined the influence of each data point on the model (support
it has been observed that more stable results for estimating vari- vectors were the data with non-zero weights), K(xi , xj ) is the kernel
able importance are achieved with a higher number (Grimm et al., function, and C is the regularization parameter, which determined
2008). the trade-off between the training errors and model complexity
The training data that were left out of the bootstrap samples (i.e., flatness of f(x)). The SMO algorithm decomposed the optimiza-
(out-of-bag (OOB) samples) were used to estimate prediction error tion problem into sub-problems, which were solved step by step
and variable importance. In error estimation, the OOB samples were (Platt, 1999). At each step, the algorithm selected two Lagrange
predicted by the respective trees and by aggregating the predic- multipliers, found their optimal values analytically, and updated
tions, the mean square error (MSEOBB ) was calculated using Eq. (2) the SVR function (Eq. (7)) to reflect the new values. The process
(Cutler et al., 2012): was repeated until the Lagrange multipliers converged.

1
N 
N

MSEOOB = (yi − ŷiOOB )

2
(2) f (x) = (˛i − ˛∗i )K(xi , xj ) + b (7)
N
i=1 i=1

where b is a constant threshold. The Gaussian radial basis kernel

where ŷiOOB is the OOB prediction for observation yi . Regarding vari-
able importance, the values of a specific predictor variable were
randomly permutated in the OOB data of a tree while the val-
ues of other predictors remain fixed. The modified OOB data were
predicted, and the differences between the MSEs obtained from
the permutated and original OOB data gave a measure of variable
importance.
3.2.2. Support vector machines for regression
Support vector machines (SVM) use kernel functions to project
the data onto a new hyperspace where complex non-linear patterns
can be simply represented (Gunn, 1998; Williams, 2011). In the
new hyperspace, SVM aims to construct an optimal hyperplane that
separates classes and creates the widest margin between their data
(i.e., classification), or that fits data and predicts (i.e., SVR) with
minimal empirical risk and complexity of the modelling function.
In this study, SVR was used. Given the training data {(xi , yi ), i = 1,
2, . . . n}, where x is a vector of the input predictors and y is the
values of SOC stocks, the SVR developed an optimal function f(x)
function of the form in Eq. (8) was used (Tien Bui et al., 2012).
2
− xi ,xj /2 2
K(xi , kj ) = exp (8)
where  is the bandwidth parameter. The best parameters C and 
obtained using the training data were 5 and 0.1, respectively. Deter-
mination of these parameters was carried out using the grid search
method (Zhuang and Dai, 2006; Kavzoglu and Colkesen, 2009).
3.2.3. Artificial neural networks
Artificial neural network algorithm simulates human learning
processes through establishment and reinforcement of linkages
between the input and output data. The linkages then connect input
and output data in the absence of training data (Campbell, 2002).
Numerous ANN algorithms have been proposed, such as Radial
Basis Function (Vojislav, 2001), Elman recurrent (Rakkiyappan and
Balasubramaniam, 2008), and Hopfield neural networks (Nguyen
et al., 2006); however, Multi-layer perceptron neural networks
(MLP Neural Nets) with back-propagation algorithm may be the
398 K. Were et al. / Ecological Indicators 52 (2015) 394–403
Fig. 2. Architecture of the MLP neural network for SOC stocks modelling.
most popular, and was selected for this study. The architecture of
the MLP Neural Nets consists of input, hidden, and output layers
(Fig. 2), each with a set of interconnected nodes (neurons) work-
ing in parallel to transform the input data into output values (Lee
and Evangelista, 2006; Conforti et al., 2014). In this context, the
neurons in the input layer were equal to the 16 predictors that
were statistically selected from the original list, while the number
of neurons in the hidden layer, which carried weights representing
the linkages between the predictors and SOC stocks, was deter-
mined using both the training and validation data. That is, values
ranging from 1 to 20 were used to build different models, the
training and prediction errors of which were calculated (Fig. 3).
The network having 2 hidden neurons and the lowest error was
selected, with the Unipolar sigmoid as the transfer function. The
output layer comprised a single neuron that represented the output
values of SOC stocks. The training phase was initiated by assigning
arbitrary connection weights. Then the algorithm fed forward the
input layer to the hidden layer. The neurons in the hidden layer
multiplied the inputs by their associated weights, summed up the
products, and processed the weighted sums using the transfer func-
tion, the results of which were propagated to the output layer (Lee
and Evangelista, 2006). The output values were compared with
the expected values in the training data, and the errors computed.
Through iterative propagation of errors back to the network, the
connection weights were automatically adjusted until the target
minimum error was attained, and the network was able to assign
correct values of SOC stocks to the training data, as well as from new
input data in the absence of training data. To achieve this, different
tests were conducted and the best learning rate, momentum, and
training time (iterations) obtained were 0.01, 0.18, and 500, respec-
tively. Finally, the trained network was used as a feed-forward
structure to produce predictions for the entire spatially continuous
data.
Fig. 3. Training and validation errors associated with a given number of neurons in
the hidden layer.
3.3. Model testing and comparison
The testing data (n = 44) was used to validate the RF, SVR, and
ANN models, and derive statistical measures to compare their per-
formance. The root mean squared error (RMSE) and mean error
(ME) were computed from the differences between the predicted
SOC stock values and measured values (Eqs. (9) and (10)), to deter-
mine the precision and bias of the predictions, respectively.
n (y − ŷ )2
i i
RMSE = (9)
1 n

n
(yi − ŷi )
ME = (10)
n
1
where ŷi is the estimated value, yi is the measured value and n is
the number of measured values in the testing data. The ME should
be close to zero, while RMSE should be as small as possible. The
coefficient of determination (R2 ) was also calculated.
3.4. Model application
We applied the output SVR, ANN, and RF models to create pre-
diction surfaces that showed the spatial distribution of SOC stocks.
Data preparations, analyses, and geovisualization were carried out
using ArcGIS® 10.1, ERDAS IMAGINE® 2013, Microsoft Excel® 2010,
Weka 3.6, and R 3.0.1 (R Core Team, 2013) with its add-in packages:
“sp”, “maptools”, “rgdal”, “randomForest”, and “raster”.
4. Results and discussion
4.1. Exploratory data analysis
Descriptive statistics of SOC stocks along with other soil
properties are presented in Table 1. SOC stocks ranged from
42.0 to 193.4 Mg C ha−1 , with a mean and median of 102.7 and
103.2 Mg C ha−1 , respectively. The standard deviation and coef-
ficient of variation were 24.6 Mg C ha−1 and 23.9%, respectively,
denoting moderate variability of SOC stocks. This can be attributed
to environmental factors, such as climate, land cover, and topogra-
phy, as well as measurement errors. The BD varied between 0.5 and
1.1 g cm−3 , and the pH between 4.8 and 7.0. The macronutrients,
including N, P, and K ranged from 0.2 to 0.9%, 8 to 62.5 me/100 g,
and 0.3 to 2.1 me/100 g, respectively, while the soil separates var-
ied from 20 to 53% for sand, 21 to 49% for silt, and 10 to 55% for
clay. For all soil properties, the mean and median values were sim-
ilar indicating normality of data distribution. Some skewness was
evident, although quite low and mostly positive. This was proba-
bly the influence of extreme data values. Similarly, kurtosis values
were low, which implied less peaked values in data distribution.
According to Table 2, Pearson’s coefficients (r) ranged between
−0.04 (sand content) and 0.74 (TN content) for the relationships
between SOC stocks and the predictors. Among the predictors, the
correlation between temperature and elevation (r = −0.99), eleva-
tion and TN (r = 0.81), temperature and band 11 (r = 0.81), elevation
and band 11 (r = −0.83), band 11 and PC1 (r = 0.82), land cover and
elevation (r = −0.83), land cover and temperature (r = 0.83), and
land cover and band 11 (r = 0.88) exceeded the threshold corre-
lation value of 0.8. Therefore, elevation, temperature, and band 11
were excluded from model building: their VIFs in regression anal-
ysis were also greater than 10 (not shown here). This reduced the
number of predictors from 19 to 16.
 K. Were et al. / Ecological Indicators 52 (2015) 394–403 399

Table 1
Descriptive statistics of SOC stocks and some soil properties in 0–30 cm depth.

Soil properties 0–30 cm

SOC (Mg ha−1 ) C (%) TN (%) P (ppm) K (me %) Ca (me %) Mg (me %) BD (g cm−3 ) pH Clay (%) Silt (%) Sand (%)

Mean 102.65 4.22 0.42 31.86 1.21 4.04 4.97 0.84 5.84 28.13 35.56 36.25
Median 103.15 4.02 0.41 30.25 1.24 4.10 5.29 0.84 5.81 27.00 36.00 36.00
SD 24.55 1.26 0.13 12.56 0.43 1.44 1.42 0.11 0.50 7.28 5.93 5.89
CV 23.91 29.84 29.64 39.43 35.23 35.58 28.59 13.18 8.64 25.87 16.68 16.24
Kurtosis 0.39 0.79 0.51 −0.75 −0.64 8.27 −0.40 0.05 −0.70 0.85 −0.40 0.31
Skewness 0.97 0.81 0.71 0.31 −0.08 1.67 −0.43 −0.20 0.18 0.79 −0.03 0.00
Range 151.43 6.86 0.67 54.50 1.86 11.00 7.16 0.60 2.19 45.00 28.00 33.00
Minimum 41.99 1.86 0.18 8.00 0.28 1.40 1.38 0.50 4.83 10.00 21.00 20.00
Maximum 193.42 8.72 0.85 62.50 2.14 12.40 8.54 1.10 7.02 55.00 49.00 53.00

4.2. Relative importance of the predictor variables The contributions of the remaining predictors to the models
were more or less the same; that is, their exclusion marginally
The increases in RMSEs as the predictors were excluded one increased the RMSEs. The importance of the predictors was judged
by one from the SVR, ANN, and RF models can be seen in Fig. 4. by the decrease in prediction accuracy after excluding each from the
Based on the magnitude of increase in RMSE, all models showed model(s) because SVR, ANN, and RF algorithms did not reveal the
TN concentration as the most important variable for explaining the functional relationships between the target and predictor variables.
spatial variations of SOC stocks. This was unsurprising for statistical This limited their interpretability, and is the reason they are often
and theoretical reasons. Statistically, the correlation found between referred to as “black box” approaches. Therefore, visualization of
SOC stocks and TN concentration was significantly high (Table 2), the prediction surfaces also helped to assess the soil–environment
which made it a good predictor for SOC stocks. The relationship relationships that explained the observed spatial patterns of SOC
between the two is well defined and has also been reported by stocks.
Chaplot et al. (2010), Phachomphon et al. (2010), and Elbasiouny
et al. (2014). Theoretically, the high correlation can be ascribed 4.3. Spatial prediction and mapping of SOC stocks
to the tight coupling of carbon and nitrogen cycles. For instance,
nitrogen supply increases the net uptake of carbon by stimulating The spatial patterns of SOC stocks predicted by SVR, ANN, and RF
biochemical determinants, including the photosynthetic enzymes models are displayed in Fig. 5. Broadly, the three prediction surfaces
(Lorenz, 2013), which in turn leads to higher input of carbon and were similar in terms of the spatial patterns of SOC stocks. There
nitrogen to the SOC pool. In addition, mineralization of organic was an increasing gradient of SOC stocks from east to west, with the
matter not only leads to the breakdown of carbon substrates and highest stocks on the western and north-western parts. This clearly
emission of CO2 , but also to the release of plant-available inorganic reflected the land cover-effect because these were areas covered by
nitrogen (Butterbach-Bahl and Dannenmann, 2012). Other nitrogen the Logoman, Nessuiet, Kiptunga, and Baraget forests. Besides land
transformations (e.g., nitrification and denitrification) also use the cover, the highly fertile Andosols, high rainfall, low temperatures,
energy supplied by carbon (Batlle-Aguilar et al., 2011). This finding and high altitudes, which favour high net primary productivity and
differs from previous studies, which for instance reported that land low SOC turnover, also explained the high carbon storage in these
use (Wiesmeier et al., 2011) and topographic attributes (Grimm parts. The lowest stocks, on the other hand, were distributed on the
et al., 2008) were the most important predictors of SOC stocks. Most eastern part, including Teret, Nessuiet, Kapkembu, Tuiyotich, and
of the past studies, however, seldom included TN concentration in Sururu locations. These were areas where plantation and indige-
distributed modelling of SOC stocks mainly because accurate and nous forests had been converted to croplands since the mid-1990s.
spatially-exhaustive information on it (and other soil parameters, Thus, the low SOC stocks was due to biomass removal after harvest-
e.g., pH, CEC, soil moisture, etc.) was lacking. ing, erosive processes, and frequent tillage, which breaks up the soil
aggregates, alters aeration, and accelerates microbial decomposi-
PC1 tion and oxidation of SOM to CO2 (Murty et al., 2002; Smith, 2008;
TWI Eclesia et al., 2012; Wiesmeier et al., 2012). The northern and south-
Rainfall eastern parts exhibited moderate to high SOC stocks. These also
Land cover were cropland-dominated areas. Higher estimates of SOC stocks in
Aspect forests and lower estimates in croplands coincide with the findings
Predictor excluded from the model

Slope of Tesfahunegn et al. (2011) in northern Ethiopia.

Curvature Table 3 shows the general statistics of the predictions by the
SVR
NDVI SVR, ANN, and RF models. The predicted minimum and mean val-
ANN
Sand ues approximated the measured ones, whereas the maximum and
RF
Silt standard deviation values slightly differed from the measured ones
Mg (cf. Table 1). The training data point with the maximum value was
Ca
probably treated as an outlier by the algorithms resulting in the
K
different maximum values.
Targeted climate change mitigation and sustainable land man-
P
agement strategies in the area will require an understanding of
pH
the spatial distribution of SOC stocks; hence, the output SOC stock
TN
map is important. The map can guide the identification of areas
13 14 15 16 17 18 19 20 21 for differential allocation of resources for carbon sequestration and
Increase in RMSE fertility management. For instance, areas with low SOC stocks, but
Fig. 4. Variable importance shown by increase in the RMSEs of the SVR, ANN, and
with good soil fertility potential may be targeted for conservation
RF models after excluding a predictor. agriculture and agro-forestry practices.
400 K. Were et al. / Ecological Indicators 52 (2015) 394–403

Fig. 5. Spatially distributed maps of SOC stocks.

4.4. Performance of the spatial models
Table 4 presents the prediction error indices derived from inde-
pendent validation of the SOC stock maps using the testing dataset.
The negative ME signs indicate that the models overestimated SOC
stocks. In particular, the RF model with an ME of −6.5 Mg C ha−1
had the highest tendency for overestimation, while SVR model with
an ME of −4.4 Mg C ha−1 showed the lowest tendency for over-
estimation. The RMSEs from the testing data varied from 14.9 to
17.6 Mg C ha−1 , which compared with those of the fitted models
(i.e., 14.5, 15.4, and 18.3 for SVR, ANN, and RF models, respectively).
This implies that the models predicted new data as precise as they
fitted the training ones. Support vector regression model had the
lowest RMSE (14.9 Mg C ha−1 ) and ME values, as well as the highest
R2 (0.6) value; hence, it was the best method to predict SOC stocks
at the unvisited locations in this context. However, ANN prediction
followed closely with RMSE, ME, and R2 values of 15.5, −4.7, and
0.6, respectively. This indicated a modest relative improvement of
 K. Were et al. / Ecological Indicators 52 (2015) 394–403 401

Table 3

1.00
20
Descriptive statistics of the SOC stocks estimated by the SVR, ANN, and RF models.

0.81
1.00
19 Model Min. Max. Mean SD

1. SVR 40.05 169.05 103.75 15.16

2. ANN 44.45 180.99 105.48 16.20

0.71 −0.99
0.82 −0.83
−0.72 1.00
3. RF 58.38 162.94 105.39 14.61
18

1.00
Table 4
17

Prediction error indices of the SVR, ANN, and RF models.

Model ME RMSEcal RMSEval R2

−0.19
0.18
0.11
0.07
1.00
16

1. SVR −4.42 14.45 14.88 0.64

2. ANN −4.71 15.39 15.46 0.61
3. RF −6.51 18.27 17.57 0.53

0.65
−0.62
−0.57
−0.04
−0.50
1.00
15

−0.83
0.83
0.88
−0.46
0.11
0.74
1.00

prediction accuracy by SVR. Thus, in other contexts, both SVR and

14

ANN models should be calibrated, and the best result applied for
spatial prediction of target soil properties. The RF model results
compare with other studies in the region (Vågen and Winowiecki,
−0.16
0.18

−0.25
0.17
−0.17
−0.25
−0.01
1.00

2013; Vågen et al., 2013), although the other studies reported

13

slightly higher R2 values than this one. This may be because of the
different extents of the study areas, topography, sampling densi-
−0.21

−0.23

0.17
−0.19
−0.12
−0.02

−0.03
1.00

−0.00

ties, or quantity and quality of the auxiliary data used. In addition,

12

these comparative results are consistent with those of Rossel and

Behrens (2010) who found that SVR outperformed RF and boosted
−0.14

−0.12
−0.12
0.12
0.04
−0.01
0.08

−0.10
−0.03
1.00

trees in estimating SOC, clay content, and pH in Australia.

11

Furthermore, the RMSEs of all models were lower than the

standard deviations of the measured values (cf. Table 1), which
0.18
0.12
−0.52
0.16

−0.21
0.44
−0.44
−0.57
−0.09

−0.05
1.00

suggested that application of auxiliary spatial data produced bet-

10

ter predictions than what was expected using the measured values
alone. Generally, the RMSE values obtained in this study reflected
−0.26

0.39
0.17
0.12
0.26

0.33
−0.04
−0.04
0.05

−0.30

0.30
1.00

the measurement, laboratory, statistical, and random errors. For

example, the soil properties used as predictors were interpolated
9

by ordinary kriging. Thus, the associated interpolation errors were

propagated to the subsequent SOC stock estimations. Retrieval of
−0.27

−0.17

0.43
−0.37

0.26
−0.43
0.41
0.47
0.05

−0.08

−0.01
1.00
0.00

auxiliary spatial data from different sources also meant different

8

data quality. Poor coverage of samples in the south-eastern most

and middle parts dominated by thick impenetrable bamboo forests
0.36

0.14
−0.12

0.41

−0.11
−0.40

−0.06

0.08

0.04
−0.06
0.01
0.03
1.00

−0.00
Correlation matrix showing the relationships between the variables used in spatial modelling.

also influenced prediction accuracy in these areas. Lastly, some

7

soil-forming factors (e.g., parent material) were not included in

the models for lack of suitable data. Thus, incorporating the miss-
0.41
−0.25

−0.22

−0.12
0.36
−0.26

0.46
−0.42
0.42
0.39
0.10

−0.07
−0.05

0.02
1.00

ing environmental data, as well as the stochastic component by

6

analysing the spatial structure of residuals with geostatistical tech-

niques (i.e., kriging) (Hengl et al., 2004, 2007) are some of the ways
0.71
0.66

0.28
−0.12

0.33
0.11

0.32
−0.32
0.34
0.21
−0.40

−0.05
−0.08
−0.03

0.10
1.00

to minimize prediction errors in future.

5

5. Conclusion
0.69
0.45
0.57
−0.17
0.38
−0.28

−0.16

0.49
0.17

0.33
−0.38
0.41
0.27
0.02

−0.08

0.01
1.00
4

The results have demonstrated that SVR with SMO algorithm

is the best for spatially predicting and mapping the patterns of
0.62
0.63
0.56

0.37

−0.12
−0.14
0.73
−0.43

0.64
−0.75
0.74
0.64
0.40
0.05

−0.30
0.01

0.06
1.00

SOC stocks in the Eastern Mau Forest Reserve, Kenya. However,

Highly correlated predictor variables are in bold.
3

due to the close performance of SVR and ANN models, we propose

that both models should be calibrated, and then the best result
0.81
−0.44

−0.11
0.38
−0.67

0.36

0.17
−0.68

−0.17
−0.64

−0.78
−0.79
0.07
0.07

−0.09

0.09
0.08

0.70
1.00

applied for spatial prediction of target soil variables in other geo-

graphical settings. Data quality cannot be overlooked in the process.
2

The results have also shown that TN is the most important vari-
able explaining the observed variability of SOC stocks in the area,
0.72
−0.28

−0.15

−0.47

0.27

0.15
−0.48
0.43

−0.46
0.52
−0.51
−0.56
0.06
0.03

0.20

−0.04

0.06
0.04

−0.10
1.00

and that contributions of the other environmental factors are only

1

marginal. Overall, the performance of the models in this study will

inform the selection of machine learning techniques for spatial pre-
19. Temperature
4. Phosphorous

14. Land cover

7. Magnesium

diction of SOC stocks plus other soil functional properties in other

11. Curvature
2. TN content

18. Elevation
5. Potassium
1. SOC stock

20. Band 11
15. Rainfall
6. Calcium

environments, while the map generated will be instrumental for

13. Aspect
Variables

12. Slope
10. NDVI

16. TWI
17. PC1
9. Sand

formulating spatially-targeted climate change mitigation and sus-

8. Silt
Table 2

3. pH

tainable land management strategies. In future, model performance

will be improved by incorporating other important environmental
402 K. Were et al. / Ecological Indicators 52 (2015) 394–403
data (e.g., parent material), as well as the stochastic component of
SOC stocks.
Acknowledgements
We thank the Research Council of Norway for funding this work
through the Norwegian University of Life Sciences. We also thank
Mr. P. Owenga for technical support, Mr. E. Thairu for driving skil-
fully in extreme weather and terrain conditions, and the three
anonymous reviewers for their constructive comments.
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