Soil Security 5 (2021) 100025

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Soil Security
journal homepage: www.sciencedirect.com/journal/soil-security

Modeling paddy field soil conditions in East Java, Indonesia

Setyono H. Adi a, b, *, Sabine Grunwald b, Chendy Tafakresnanto a, Hendri Sosiawan a
a
Indonesian Agency for Agricultural Research and Development, the Ministry of Agriculture Republic of Indonesia, Indonesia
b
Soil and Water Sciences Department, University of Florida, USA

A R T I C L E I N F O A B S T R A C T

Keywords: Knowledge of soil conditions is a critical factor of effective land management to achieve optimum ecosystem
Soil security services in agriculture. Digital soil modeling that incorporates soil spectral data has become a cost-efficient
Agricultural soil modeling method compared to traditional wet-chemical soil analysis to produce high quality soil management data at
Soil VNIR spectroscopy
the regional level. This research objective was to develop soil property prediction models to assess the charac­
Soil property prediction
Soil data fusion
teristics of paddy field soil conditions in East Java, Indonesia. This study examined the utilization of a hybrid
two-step regression (2Step-R) soil modeling approach that incorporates categorical soil-environmental variables
and continuous visible-near-infrared (VNIR) spectral data. The integrative 2Step-R method was implemented in
two modes—Partial Least Square Regression, PLSRmod, and Sparse Bayesian Infinite Factor, SBIFmod—with
‘mod’ referring to the fusion of important categorical soil-environmental parameters and soil VNIR spectral data.
This research successfully developed reliable prediction models for soil organic carbon, nitrogen (N), pH, sum of
bases (SB), and cation exchange capacity in the study area, with acceptable model performance (performance to
interquartile ratio or RPIQ 1.77 to 2.54; performance to deviation ratio or RPD 1.45 to 1.89; and coefficient of
determination or R2 0.53 to 0.72). The fused soil-environmental and VNIR spectral data approach (2Step-R)
showed markedly improved model performances when compared to models that solely used VNIR spectra data
(PLSR) for all modeled soil properties. This research underpins the utilization of cost-effective soil modeling to
reveal existing soil conditions in securing soil ecosystem services for intensive agriculture in data sparse regions
such as Indonesia.

1. Introduction
Soil provides physical and nutrient support for food crop produc­
tivity and is critically important for agriculture (Koch et al., 2013).
Agricultural soil ecosystem services are influenced by the variation and
interaction between soil properties, such as soil organic carbon (SOC),
nitrogen (N), pH, exchangeable bases (SB), and cation exchange ca­
pacity (CEC) (Adhikari and Hartemink, 2016; Lal, 2006). Soil degrada­
tion due to intensive agriculture limits agricultural production and
threatens food security (Lal, 2004; Smith et al., 2016). This problem
could then escalate that lead to wicked interconnected environmental
problems, such as food, water, and energy crisis, that requires integral
understanding of soil in order to solve complex environmental dilemmas
(Bouma and McBratney, 2013; Grunwald et al., 2017). Therefore, stra­
tegic soil management to improve soil quality is required (Lal, 2010;
Mizuta et al., 2018). As part of soil security dimensions, accurate soil
condition information is required for effective land management in
securing soil ecosystem services in the agricultural domain (Field, 2017;
McBratney et al., 2014). But in most cases, this effort is impeded by the
high cost of traditional soil data acquisition (Grunwald et al., 2015).
Soil modeling has been extensively studied to support soil manage­
ment (Gredilla et al., 2016; Soriano-Disla et al., 2014). Soil can be
modeled utilizing external environmental variables through soil facto­
rial modeling (Grunwald et al., 2011; McBratney et al., 2003), internal
soil parameters through soil spectroscopy (Bellon-Maurel and McBrat­
ney, 2011; Stenberg et al., 2010), or the combination of soil factorial and
spectroscopy modeling (Adi and Grunwald, 2020; Grunwald et al.,
2015). Extensive studies have demonstrated that reliable soil property
predictions can be achieved utilizing various soil modeling methods,
particularly for soil total and organic carbon (Dotto et al., 2017, 2018;
Gray et al., 2015; Knox et al., 2015; Pinheiro et al., 2017; Xiong et al.,
2014). However, soil modeling applications in support of soil manage­
ment in Indonesia have been underexplored. Recent soil modeling
studies utilizing the soil visible-near infrared (VNIR) spectroscopy
method for SOC predictions in Lombok (island), Indonesia, showed
promising prediction model performance results, with cross-validation

* Corresponding author at: Indonesia Agroclimatology and Hydrology Research Institute, Jalan Tentara Pelajar 1a, Bogor, West Java, 16111, Indonesia.
E-mail address: setyonohari@pertanian.go.id (S.H. Adi).

https://doi.org/10.1016/j.soisec.2021.100025
Received 28 July 2021; Received in revised form 3 November 2021; Accepted 30 November 2021
Available online 3 December 2021
2667-0062/© 2021 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license
(http://creativecommons.org/licenses/by-nc-nd/4.0/).
S.H. Adi et al.
Fig. 1. Map of study area and soil sampling locations in East Java, Indonesia (data source: Hikmatullah et al., 2016).
coefficient of determination (R2) and ratio of performance to deviation
(RPD) of about 0.7 and 2.0, respectively (Kusumo et al., 2018a,2018b).
Though these studies suggest that VNIR is promising for modeling of
other soil properties in Indonesia it has rarely been used at all.
The research presented in this paper focuses on soil security in
agricultural land at regional scale. We aimed to assess agricultural soil
conditions in East Java, Indonesia. Soil prediction models were devel­
oped following the integrative 2Step-R method by Adi and Grunwald
(2020) by utilizing two latent variable methods, including the Partial
Least Squares Regression (PLSR) (De Jong, 1993) and the Sparse
Bayesian Infinite Factor regression (SBIF) (Bhattacharya and Dunson,
2011). Proper inclusion of important soil-environmental parameters in
the modeling, including soil order, topographical landform, parent
material, and soil sample depth, was implemented to improve model
performances. The research objectives were to (1) develop and evaluate
soil property prediction models for SOC, N, pH, SB, and CEC using VNIR
spectra in East Java, Indonesia, and (2) assess the characteristics of the
existing East Java paddy field soil conditions based on the included
modeling parameters.
2. Material and methods
2.1. Study area
Geographically, East Java province, Indonesia, is located between
110◦ 54′ and 114◦ 37′ east longitude and between 8◦ 48′ and 6◦ 44′ south
latitude, with a total area of about 42,000 km2. East Java geology is
dominantly volcanic rocks (63%), followed by alluvium (15%), lime­
stone (12%), and sedimentary rocks (11%) (Sigit, 1965). This region is
classified into two Köppen climatic zones: a tropical monsoon region
(Am) in western East Java, and a tropical wet savanna region (Aw) in
eastern East Java (Kottek et al., 2006). The last decade weather data
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Soil Security 5 (2021) 100025
(2006 – 2016) in the study area showed an average annual rainfall of
about 2050 mm per year, with an average minimum and maximum
annual temperature of about 22 and 34 ◦ C, respectively (Indonesia
Statistics Agency, 2016). Based on the 2009 Java paddy-rice fields map,
paddy-rice cultivation accounted for 24% of the East Java province total
area (Indonesia Center for Agricultural Land Resources Research and
Development, 2009). The major soil orders in East Java agricultural
fields were Vertisols (44%), followed by Inceptisols (32%), Andisols
(15%), and fractions of Mollisols, Entisols, and Ultisols (totaling about
9%) (Indonesia Center for Agricultural Land Resources Research and
Development, 2000). Furthermore, the East Java agricultural fields were
located in the regions with elevations within the range of 0 to 1280 m,
with median and mean elevations of about 56 and 108 m, respectively
(Jarvis et al., 2008). The map of the study area is presented in Fig. 1.
2.2. Materials
We collected soil samples from East Java paddy fields during the
2016 agricultural soil survey project (Hikmatullah et al., 2016). The soil
data collection was performed following the representative soil sam­
pling design. Sampling locations in the survey region were determined
to represent each unique polygon area derived from the intersection of
soil forming factor spatial data, including climate classification, land use
(agricultural field), topographic factor (slope and landform), and parent
material (Hikmatullah et al., 2016). There was a total of 316 soil samples
collected from 170 unique observation sites, with up to 6 sample depths
down to 1.2 m soil depth (each layer is about 20 cm in depth). The
number of samples that were collected from the first (i.e., 0 – 20 cm)
down to the sixth soil sample depth (i.e., 100 – 120 cm) are 170 (54%),
55 (17%), 47 (15%), 33 (10%), 9 (3%), and 2 (1%), respectively. Five
laboratory-measured soil properties were considered in this research,
including soil organic carbon (SOC,%), nitrogen (N,%), pH
S.H. Adi et al. Soil Security 5 (2021) 100025

Table 1 (dimensionless), sum of bases (SB, cmolc kg− 1; i.e., the sum of Ca, Mg, K,
The list of unique combination between soil order, landform, and parent ma­ and Na concentrations), and cation exchange capacity (CEC, cmolc
terial classification, and the number of samples within each category. kg− 1). SOC was measured using the Walkley and Black method, while N
Soil order Landform Parent material Maximum Number of was extracted based on the Kjeldahl method (American Society of
sample depth Samples Agronomy and Soil Science Society of America, 1982; Black, 1965).
(cm) Furthermore, pH was measured based on the diluted soil samples in
Andisols Plains* Mixed grain 40 (2 layers) 5 deionized water at 1:5 ratio, while SB and CEC were determined by
unconsolidated reacting each sample with 1 Normal ammonium acetate solution at pH 7
sediments (sumx)
(Hikmatullah et al., 2016).
Andisols Plains Intermediate volcanic 100 (5 layers) 54
rocks (vi__) Soil spectra for the chemometric modeling were measured on air-
Andisols Open Intermediate volcanic 120 (6 layers) 34 dried (16 h) and sieved (2 mm) soil samples. The 16 h air drying at
slopes rocks (vi__) room temperature and 2 mm sieving procedures on the field-dry
Andisols Mid Intermediate volcanic 100 (5 layers) 5 sampled soils were performed to achieve sample uniformity before the
slopes rocks (vi__)
Entisols Plains Mixed grain 20 (1 layer) 1
measuring of VNIR spectra. Measurements were performed using the
siliciclastic sediments HR-1024i spectrometer (Spectra Vista Corporation, Poughkeepsie, NY)
(ssmx) with three different resolutions, that is, 1.5 nm at 350 – 1000 nm, 3.8 nm
Entisols Plains Mixed grain 80 (4 layers) 21 at 1000 – 1890 nm, and 2.5 nm at 1890 – 2500 nm wavelength, with a
unconsolidated
total of 979 VNIR spectrum bands. Ten automatic internal measure­
sediments (sumx)
Entisols Plains Intermediate volcanic 80 (4 layers) 11 ments taken for each soil samples at two different random probe posi­
rocks (vi__) tions were averaged to reduce spectral noises. The averaged-spectra was
Entisols Open Mixed grain 100 (5 layers) 5 the final spectra used the statistical modeling. In addition, a Spectralon
slopes unconsolidated white reference was used for calibration prior to each of the sample
sediments (sumx)
spectral measurements.
Entisols Open Intermediate volcanic 40 (2 layers) 2
slopes rocks (vi__) This research considered four environmental variables as ancillary
Inceptisols Plains Mixed grain, mixed 20 (1 layer) 3 predictors for soil spectroscopy modeling. These variables include soil
sedimentary rocks taxonomical order (Indonesia Center for Agricultural Land Resources
(smmx)
Research and Development, 2000), Digital Elevation Model (DEM)-­
Inceptisols Plains Mixed grain 20 (1 layer) 3
siliciclastic sediments generated landform based on the topographic position index (Jarvis
(ssmx) et al., 2008), parent material (Hartmann and Moosdorf, 2012), and
Inceptisols Plains Mixed grain 80 (4 layers) 25 sample depth classification (Hikmatullah et al., 2016). These variables
unconsolidated were combined prior to the analysis to form a new classification based
sediments (sumx)
on the unique combination between soil order, landform, parent mate­
Inceptisols Plains Intermediate volcanic 100 (5 layers) 29
rocks (vi__) rial, and sample depth classification (Table 1). Sample depth was only
Inceptisols Open Intermediate volcanic 80 (4 layers) 5 used in SOC modeling.
slopes rocks (vi__) Soil parameters, topographical landform, and parent material clas­
Inceptisols High Mixed grain 80 (4 layers) 4
sification were included as auxiliary predictor variables in the soil
ridges unconsolidated
sediments (sumx)
attribute modeling because these variables potentially contain impor­
Vertisols Plains Pure carbonate 50 (2 layers) 2 tant information to improve the prediction model accuracies. These
sedimentary rocks three categorical variables are part of the soil forming factors included in
(scup) the STEP-AWBH soil property modeling framework proposed by
Vertisols Plains Mixed grain, mixed 80 (4 layers) 5
sedimentary rocks
(smmx) Table 3
Vertisols Plains Mixed grain 80 (4 layers) 91 Spearman’s correlation coefficients among the paired soil property data from the
unconsolidated East Java agricultural fields (N: 316; data source: Hikmatullah et al. (2016)).
sediments (sumx)
Vertisols Plains Intermediate volcanic 20 (1 layer) 4 Soil property SOC N pH SB CEC
rocks (vi__)
Organic carbon (SOC,%) 1.00 – – – –
Vertisols Open Mixed grain 100 (5 layers) 7
Nitrogen (N,%) 0.96* 1.00 – – –
slopes unconsolidated
pH 0.05* 0.04* 1.00 – –
sediments (sumx)
Sum of bases (SB, cmolc kg− 1) 0.22* 0.19* 0.77* 1.00 –
Note “__” means no further sub classes. Cation exchange capacity (CEC, cmolc 0.26* 0.25* 0.55* 0.86* 1.00
kg− 1)

* Statistically significant with p < 0.05.

Table 2
Descriptive statistics of the soil property data from the East Java agricultural fields (N: 319; data source: Hikmatullah et al. (2016)).
Descriptive statistics SoilOrganic carbon(%) Nitrogen(%) pH Sum of bases(cmolc kg− 1) Cation exchange capacity(cmolc kg− 1)

Minimum 0.08 0.01 4.49 6.66 4.11

1st quartile 0.56 0.06 6.24 20.23 15.65
Median 0.92 0.09 6.66 25.79 23.97
3rd quartile 1.31 0.13 7.20 30.64 41.44
Maximum 5.45 0.45 8.66 69.03 131.06
Mean 1.06 0.10 6.70 28.91 25.63
Standard deviation 0.74 0.06 0.73 17.51 7.98
Coefficient of variation 0.70 0.61 0.11 0.61 0.31
Skewness 2.20 1.51 − 0.04 1.09 0.46
Skewness (log-transformed) − 0.41 − 0.57 − 0.04 − 0.50 0.46

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S.H. Adi et al. Soil Security 5 (2021) 100025

Fig. 2. The average visible/near-infrared reflectance profiles for each soil order at different soil depths in East Java agricultural fields (N = 316).

Table 4
The model validation performance metrics of the three chemometric methods for soil property predictions in East Java agricultural fields.
Metrics SOC N pH SB CEC Mean Min. Median Max.
(%) (%) (cmolc kg− 1) (cmolc kg− 1)

R2
PLSR Std 0.64 0.43 0.44 0.35 0.69 0.51 0.35 0.44 0.69
PLSRmod 0.71 0.58 0.53 0.62 0.72 0.63 0.53 0.62 0.72
SBIFmod 0.59 0.54 0.36 0.64 0.57 0.54 0.36 0.57 0.64
PE
PLSR Std 0.11 0.16 0.14 0.12 0.11 0.13 0.11 0.12 0.16
PLSRmod 0.08 0.12 0.13 0.13 0.11 0.11 0.08 0.12 0.13
SBIFmod 0.10 0.10 0.15 0.13 0.15 0.13 0.10 0.13 0.15
RPD
PLSR Std 1.67 1.32 1.33 1.24 1.80 1.47 1.24 1.33 1.80
PLSRmod 1.85 1.55 1.45 1.62 1.89 1.67 1.45 1.62 1.89
SBIFmod 1.55 1.48 1.25 1.66 1.52 1.49 1.25 1.52 1.66
RPIQ
PLSR Std 2.10 1.80 1.79 1.72 2.50 1.98 1.72 1.80 2.50
PLSRmod 1.77 1.83 1.91 2.46 2.54 2.10 1.77 1.91 2.54
SBIFmod 1.28 1.63 1.69 2.55 1.95 1.82 1.28 1.69 2.55

Abbreviations: R2, coefficient of determination; PE, percent errors; RPD, ratio of performance to deviation; RPIQ, ratio of performance to interquartile range; SOC, soil
organic carbon, N, soil Kjeldahl nitrogen; SB, soil sum of bases; CEC, soil cation exchange capacity; PLSR Std, standard Partial Least Squares Regression; PLSRmod,
modified PLSR; SBIFmod, modified Sparse Bayesian Infinite Factor.

Grunwald et al. (2011). Other STEP-AWBH factors including the for SOC predictions, because it is known to vary with soil depth (Pin­
ecological (E), climatic (A and W), biotic (B) and human factor (H; e.g., heiro et al., 2017).
land use) were not included in this research because the majority of
samples were collected from the region with similar ecological, climate, 2.3. Methods
and land use classification (i.e., intensive paddy rice agriculture with
commonly paddy-paddy-maize annual cropping pattern, and similar 2.3.1. preprocessing
fertilizer application and levels). Furthermore, soil sample depth clas­
sification was also utilized as an ancillary predictor variable specifically Data preprocessing for the chemometric modeling was performed

4
S.H. Adi et al.
Fig. 3. Validation model performance index (MPI) of the three chemometric models, the Partial Least Squares Regression (PLSR), modified PLSR (PLSRmod), and
modified Sparse Bayesian Infinite Factor model (SBIFmod), for soil organic carbon (SOC), nitrogen (N), pH, sum of bases (SB), and cation exchange capacity (CEC)
predictions. Three box plots on the right-hand side of the figure summarize the MPI distribution of each chemometric models.
utilizing R statistical software (R Core Team, 2017). Continuous soil
property data were log-transformed and normalized to the mean of
0 and the standard deviation of 1. Furthermore, soil spectra were
noise-filtered using the Savitzky-Golay algorithm by utilizing the
“signal” package in R (Savitzky and Golay, 1964; Signal Developers,
2014). The filtered spectra were averaged for each 10 nm spectral band
and centered to the mean of 0. Moreover, all spatial data were projected
into the Asia Lambert Conformal Conic projection prior to the data ex­
tractions. The landform classification was generated from the 90 meter
resolution Shuttle Radar Topography Mission (SRTM) DEM utilizing
“raster” and “RSAGA” packages in R (Brenning, 2008; Hijmans, 2016;
Jarvis et al., 2008). Other spatial data (i.e., soil order, parent material,
and soil layer depth) were used as is without any modification. More­
over, the ancillary spatial data, including soil order, landform, and
parent material classification, were extracted into each soil observation
geolocation utilizing the “raster” package in R (Hijmans, 2016).
2.3.2. Statistical analysis
Chemometric models for East Java agricultural soil property pre­
dictions were developed following the integrative 2Step-R modeling
method (Adi and Grunwald, 2020). Categorical soil-environmental
variables and continuous VNIR spectral data served as input data to
predict each of the soil properties (SOC, N, pH, SB, and CEC) utilizing the
hybrid 2Step-R method. In general, the 2Step-R method implements a
two steps regression procedure utilizing two different statistical pre­
diction models aimed to improve model prediction performances by
integrating VNIR spectra (continuous data) with important environ­
mental variables (categorical data). The first regression process models
continuous variables where the output is then utilized as input along
with the categorical variables in the second regression process. These
two regression processes can be performed in reverse order. In this
research, two 2Step-R models were developed. The first model
(PLSRmod) utilized PLSR (De Jong, 1993) and Ridge Regression (Hoerl,
1962; Hoerl and Kennard, 1970) to handle VNIR data (continuous) and
environmental variables (categorical), respectively. The “pls” and
“glmnet” packages were utilized to implement PLSR and Ridge Regres­
sion method in R (Friedman et al., 2010; Wehrens and Mevik, 2007). The
second 2Step-R model (SBIF mod) utilized SBIF (Bhattacharya and
Dunson, 2011) and Bayesian Multiple Linear Regression Analysis
(Bayesian MLRA). These models were implemented in R following the
procedure published by Bhattacharya and Dunson (2011), with some
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Soil Security 5 (2021) 100025
modifications to integrate Bayesian MLRA in the 2Step-R procedure.
Details about the 2Step-R method can be found in (Adi and Grunwald,
2020). The model performances were assessed by comparing soil pre­
diction performances from these two 2Step-R models with prediction
performances derived solely from VNIR data and the PLSR method.
2.3.3. Model development and prediction performance assessments
Spearman’s correlation analysis was used to assess the relationship
between soil properties prior to the chemometric modeling. The soil
chemometric modeling was performed through model development
(calibration) and evaluation (validation) processes. Observation data
were systematically split into two datasets prior to the chemometric
modeling. These datasets include the calibration dataset for model
development and the validation dataset (i.e., independent dataset) for
model performance evaluations. The ratio of the calibration to the
validation dataset was 2 to 1 according to suggestions by Franklin
(2010). Furthermore, the systematical data split was performed inde­
pendently for each soil property modeling, such that each soil property
has its own calibration and validation set. This study considered each
model to be independent under the assumption that each soil property
has its own data pattern that might differ from other properties. The
systematic data splitting was implemented using an iterative procedure
on the ordered soil property from lowest to highest values. For each
three-consecutive ordered values in each iteration, the first observation
was assigned as the validation set, while the other two observations
were flagged as the calibration set. This systematic data splitting was
performed to ensure all values within the sampled field data ranges were
captured by the developed soil prediction models. The calibration
dataset of each soil property was also used for 10-fold cross-validation of
the standard PLSR and PLSRmod. These cross-validations were per­
formed internally by the corresponding R packages (i.e., “pls” for PLSR
and “glmnet” for RR in the PLSRmod) to find the optimal number of
latent variables (PLSR) and ridge constant (RR) that minimized the Root
Mean Squared Error of Predictions (RMSEP) (Friedman et al., 2010;
Mevik and Wehrens, 2018). In addition, the number of latent variables
for the SBIFmod was calculated within the Gibbs simulation, with 3000
iterations.
This research utilized four different metrics for validation model
performance evaluations: the coefficient of determination (R2), predic­
tion percent errors (PE), ratio of performance to deviation (RPD), and
ratio of performance to interquartile range (RPIQ). The R2 was used to
S.H. Adi et al. Soil Security 5 (2021) 100025

Fig. 4. Calibration plots comparing the predicted soil property values generated from the PLSRmod models (y-axis) and the laboratory-measured soil property values
(x-axis).

measure the percent variation explained by the model, while PE was interquartile range of the independent validation dataset, respectively
calculated based on the inverse of the range to error ratio (RER− 1) (Bellon-Maurel et al., 2010; Chang et al., 2001). All the performance
(Islam et al., 2003). Furthermore, RPD and RPIQ were used to measure metrics were calculated based on the back-transformed data, that is, in
the prediction error spread compared to the standard deviation and the original measurement unit of each soil property. This research also

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S.H. Adi et al. Soil Security 5 (2021) 100025

Fig. 5. Validation plots comparing the predicted soil property values generated from the PLSRmod models (y-axis) and the laboratory-measured soil property values
(x-axis).

implemented the model performance index (MPI) to summarize the 3. Results and discussion
resulted model performance metrics (Adi and Grunwald, 2020).
3.1. Descriptive statistics and correlations among soil properties

The summary statistics of the soil property data and the Spearman’s
correlation among the paired soil properties are presented in Table 2 and

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Fig. 6. The PLSRmod model categorical variable coefficients for soil organic carbon predictions. Each point on the x-axis represents unique combination of soil order,
landform, parent material, and soil depth class category (I – VI: soil depth class, sc: carbonate sedimentary rocks, sm: mixed sedimentary rocks, ss: siliciclastic
sedimentary rocks, su: unconsolidated sediments, vi: intermediate volcanic rocks, pu: pure carbonates, mx: mixed grain, __: no data).

Fig. 7. The PLSRmod model categorical variable coefficients for soil Kjeldahl nitrogen prediction. Each point on the x-axis represents unique combination of soil
order, landform, and parent material category (sc: carbonate sedimentary rocks, sm: mixed sedimentary rocks, ss: siliciclastic sedimentary rocks, su: unconsolidated
sediments, vi: intermediate volcanic rocks, pu: pure carbonates, mx: mixed grain, __: no sub class).

Table 3. Overall, values of the coefficient of variation (CV) show the low
relative variability (CV < 1) for all soil properties within the East Java
agricultural soil sample set. Soil property data were highly skewed
(skewness > 1), especially for SOC, N, and SB. Furthermore, on average,
the soil sample data show a relatively low SOC and N content, a slightly
acidic soil pH, and a medium SB and CEC in the East Java agricultural
fields. The variability of the soil attribute values in this research are
lower (i.e., CV < 1 for all soil attributes) compared with another soil
spectroscopy modeling study in the region with similar equatorial
climate but different dominant soil order (i.e., Ultisols) by Pinheiro
et al. (2017) (i.e., CV > 1 for SOC, pH, CEC, and SB). This low variation
in soil attribute values could be due to soil samples that were collected
from a region with similar land use (i.e., intensive agriculture) and
landform (i.e., predominantly flat) (Hikmatullah et al., 2016).
The Spearman’s correlation coefficients among the paired soil
properties are presented in Table 3. The correlation value shows a
significantly high correlation between SOC and N (r = 0.96, p < 0.05).
Soil organic matter is the major source of soil organic nitrogen, such that
a linear relationship between SOC and N was expected (Stenberg et al.,
2010). Furthermore, relatively high and significant correlations were
also detected among paired pH, SB, and CEC (r > 0.50; p < 0.05). CEC
measures the abundance of cation exchange sites in soils, such that soil
with higher CEC holds more exchangeable cations (SB) (Helling et al.,
1964). Heiling et al. (1964) also argued that the concentration of
hydrogen ions (H+) in soil, which is represented by pH values, could also
influence CEC and SB, as a high concentration of H+ occupies the
available cation exchange sites, reducing the capacity of soil to hold the
exchangeable cations. Moreover, there were no correlations identified
between SOC and pH (r < 0.10; p > 0.05; Table 3), while low but sig­
nificant positive correlations were detected between SOC and both SB
and CEC (r of about 0.20; p < 0.05; Table 3). The low Spearman’s cor­
relation values between SOC and both SB and CEC could be due to the
low variation of these soil attribute values (CV < 1, Table 2).

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Fig. 8. The PLSRmod model categorical variable coefficients for soil pH prediction. Each point on the x-axis represents unique combination of soil order, landform,
and parent material category (sc: carbonate sedimentary rocks, sm: mixed sedimentary rocks, ss: siliciclastic sedimentary rocks, su: unconsolidated sediments, vi:
intermediate volcanic rocks, pu: pure carbonates, mx: mixed grain, __: no sub class).

Fig. 9. The PLSRmod model categorical variable coefficients for soil sum of bases prediction. Each point on the x-axis represents unique combination of soil order,
landform, and parent material category (sc: carbonate sedimentary rocks, sm: mixed sedimentary rocks, ss: siliciclastic sedimentary rocks, su: unconsolidated
sediments, vi: intermediate volcanic rocks, pu: pure carbonates, mx: mixed grain, __: no sub class).

3.2. Quantitative description of the soil spectra
The average VNIR reflectance profiles for each soil order at different
soil depths in the study area are presented in Fig. 2. Overall, similar
VNIR spectral curvatures were observed for all soil orders, with
noticeable differences in the reflectance magnitude. Prominent spectral
absorptions at the VNIR region near 1400, 1900, and 2200 nm were
detected in all of the spectral profiles. Unique reflectance profiles were
observed for each different soil order at different soil depths, indicating
unique properties of soil order at different soil horizons. Some over­
lapping spectral profiles within the same soil orders were also identified,
particularly for soil samples between 60 – 80 and 80 – 100 cm depths for
Andisols, and between 40 – 60 and 60 – 80 cm depths for Entisols. These
overlapping spectra could indicate a thick soil horizon (i.e., more than
20 cm) with relatively homogenous soils between two consecutive soil
layer depths. Moreover, a positive relationship between soil reflectance
values and sample depths were identified within the visible spectra re­
gion (i.e., less than 700 nm wavelength), except for Inceptisols. A similar
trend was also found in another study by Pinheiro et al. (2017), indi­
cating lower organic carbon content (i.e., lighter soil color) at the deeper
soil samples.
3.3. Chemometric model evaluations for agricultural soil property
predictions
The model validation performance metrics of the three chemometric
methods for soil property predictions are presented in Table 4. In gen­
eral, the median values of the performance metrics show better pre­
diction performances of the modified latent variables models (i.e., the
PLSRmod and SBIFmod) compared with the standard PLSR models,
particularly in terms of the validation R2 (i.e., median R2 > 0.50) and the
validation RPD (i.e., median RPD > 1.40). The PLSRmod models were
capable of improving the standard PLSR model prediction performances
for all soil properties, most noticeably for SOC, N, pH, and SB pre­
dictions, with model validation Root Mean Squared Error (RMSE) value
0.49% for SOC, 0.04% for N, 0.46 for pH, 4.11 cmolc∙kg− 1 for CEC, and

9
S.H. Adi et al. Soil Security 5 (2021) 100025

Fig. 10. The PLSRmod model categorical variable coefficients for soil cation exchange capacity prediction. Each point on the x-axis represents unique combination of
soil order, landform, and parent material category (sc: carbonate sedimentary rocks, sm: mixed sedimentary rocks, ss: siliciclastic sedimentary rocks, su: uncon­
solidated sediments, vi: intermediate volcanic rocks, pu: pure carbonates, mx: mixed grain, __: no sub class).

Fig. 11. The PLSRmod model continuous variable coefficients for soil organic carbon prediction, superimposed with the known vibrational bond spectral signatures
(Demattê and da Silva Terra, 2014; Stenberg et al., 2010; Viscarra-Rossel et al., 2009).

10.78 cmolc∙kg− 1 for SB. However, prediction accuracy improvements
from the SBIFmod models compared with the standard PLSR models
were only identified for N and SB predictions.
Recent VNIR spectroscopy studies to predict topsoil SOC using the
PLSR model in Lombok (island), Indonesia, located further east of the
study area, showed decent prediction accuracies with cross-validation
R2 and RPD of about 0.76 and 2.00, respectively (Kusumo et al.,
2018a, 2018b). Furthermore, a VNIR study to predict soil properties
using PLSR in Brazil with the same tropical climate as in our study region
showed a prediction validation R2 (and RPD; RPIQ) for SOC, pH, SB, and
CEC of about 0.71 (1.84; 1.05), 0.40 (1.18; 1.49), 0.17 (1.00; 0.00), and
0.68 (1.17; 0.82), respectively (Pinheiro et al., 2017). Another similar
study on tropical Brazilian soils but using a different statistical predic­
tion method (i.e., Support Vector Machine with linear Kernel function),
showed a prediction validation R2 (and RPIQ) for SOC, pH, SB, and CEC
of about 0.65 (2.28), 0.24 (1.81), 0.42 (1.99), and 0.72 (2.40), respec­
tively (Terra et al., 2015). A more general literature review showed the
median validation R2 for SOC, N, pH, and CEC predictions using VNIR
spectra of about 0.83, 0.57, 0.79, and 0.84, respectively (Soriano-Disla
et al., 2014). Therefore, these studies suggest that the chemometric
models in this research produced comparable soil property prediction
performances well within the results of the previous VNIR spectroscopy
studies. A similar tendency of relatively better SOC and CEC prediction
accuracies compared to N, pH, and SB predictions was also observed.
The MPI values for each of the chemometric models for soil property
predictions are presented in Fig. 3. In general, the three box plots on the
right-hand side of the figure show that both the 2Step-R models (i.e.,
PLSRmod and SBIFmod) produced better soil property prediction per­
formances compared with the standard PLSR models. Furthermore, the
PLSRmod gained slightly better prediction performances compared to
the SBIFmod. For all soil properties, prediction accuracies within the
range of “acceptable” MPI were achieved by using the modified latent
variable methods, except for the “non-reliable” pH prediction model
using the SBIFmod. Noticeable PLSRmod model performance

10
S.H. Adi et al. Soil Security 5 (2021) 100025

Fig. 12. The PLSRmod model continuous variable coefficients for soil Kjeldahl nitrogen prediction, superimposed with the known vibrational bond spectral sig­
natures (Demattê and da Silva Terra, 2014; Stenberg et al., 2010; Viscarra-Rossel et al., 2009).

Fig. 13. The PLSRmod model continuous variable coefficients for soil pH prediction, superimposed with the known vibrational bond spectral signatures (Demattê
and da Silva Terra, 2014; Stenberg et al., 2010; Viscarra-Rossel et al., 2009).

improvements compared with the standard PLSR models were identified
for the prediction of N (“non-reliable” to “acceptable”), pH (“fair” to
“acceptable”), and SB (“fair” to “acceptable”). The PLSRmod models
outperformed the standard PLSR models for all soil property predictions,
except for CEC predictions where similar “acceptable” MPIs were ach­
ieved. These results suggest that among the three chemometric models,
the PLSRmod method performed the best for soil property predictions in
the East Java agricultural fields. Furthermore, the calibration and vali­
dation plots comparing the predicted soil property values generated
from the modified PLSR models and the laboratory-measured soil
property values are presented in Fig. 4 and Fig. 5, respectively. Each soil
property prediction trend line in Fig. 5 shows the tendency of the
PLSRmod models to overestimate low soil property values but under­
estimate the high values. Note that soil property values are presented in
its original measurement units (non-transformed).
The categorical and continuous variable coefficient values of the
PLSRmod models are presented in Fig. 6 to Fig. 10. In general, the cat­
egorical variable coefficient profile for each soil property prediction
model showed distinctive coefficient values for each discrete variable
category, although similarities between some classes were also identi­
fied (Fig. 6 to Fig. 10). The additional soil depth classification for the
SOC prediction was able to reveal the trend of SOC content variations at
different soil depth, in which deeper soil samples tend to have low SOC
content (i.e., lower coefficient values) (Fig. 6). This finding is in agree­
ment with previous soil spectroscopy modeling study by Pinheiro et al.
(2017). However, higher coefficient values at deeper soil layers (i.e.,
more than 80 cm soil depth, as represented by layer V and VI) were also
observed for Andisols with intermediate volcanic rock (vi) parent ma­
terial (Fig. 6). This unique pattern indicates an upbuilding pedogenesis
soil formation that is common in the region with relatively high volcanic
activities, such as in the East Java province. Region with upbuilding
pedogenesis could have soil horizon with high SOC content (i.e., A ho­
rizon) buried at the deeper soil depth caused by significant episodic
surface material accumulation during volcanic activities (Lowe and
Tonkin, 2010; Tanikawa et al., 2014). Furthermore, distinct coefficient
values were also observed for each categorical variable category for N,

11
S.H. Adi et al. Soil Security 5 (2021) 100025

Fig. 14. The PLSRmod model continuous variable coefficients for soil sum of bases prediction, superimposed with the known vibrational bond spectral signatures
(Demattê and da Silva Terra, 2014; Stenberg et al., 2010; Viscarra-Rossel et al., 2009).

Fig. 15. The PLSRmod model continuous variable coefficients for soil cation exchange capacity prediction, superimposed with the known vibrational bond spectral
signatures (Demattê and da Silva Terra, 2014; Stenberg et al., 2010; Viscarra-Rossel et al., 2009).

pH, SB, and CEC prediction models, although there was no evidence of
an observable unique pattern (Fig. 7Fig. 8Fig. 9 to Fig. 10). A prominent
coefficient value for each categorical variable class was identified for
CEC prediction (Fig. 10), highlighting the significance of soil order,
landform, and parent material variations for the CEC prediction.
The continuous variable coefficient values of the PLSRmod models
are presented in Fig. 11 to Fig. 15. Some of the observed important
spectral bands for each predicted soil attribute were not exactly aligned
to the known chemical bonding spectral signatures due to the averaged
spectra. In general, the PLSRmod models identified unique coefficient
value profiles for each soil attribute model. The visible spectra regions
between 350 and 700 nm wavelength were important for all soil prop­
erty predictions, suggesting the importance of soil color to the soil
attribute predictions in East Java agricultural fields. This finding is
consistent with the noticeable positive relationship between soil depth
and soil spectra in the visible region, as presented in Fig. 2. However, the
PLSRmod models also identified important VNIR bands that coincided
with less commonly known spectral signatures in the soil spectroscopy
literature (e.g., spectral region at near 1250 nm wavelength) which
likely contributed to model uncertainties.
The PLSRmod model for SOC predictions (Fig. 11) identified several
important spectral band predictors that coincided with the known car­
bon vibrational bond spectral signatures (i.e., C–H, C–O, C = O),
particularly in the region near 850 and 1170 nm (alkyl), 1450 nm
(carboxylic acids), 1650 nm (aromatics), 1730 – 1850 and 2300 – 2470
nm (methyls), 1960 nm (phenolics), 2030 nm (amides), 2140 nm
(polysaccharides), 2275 nm (aliphatic), and 2380 nm (carbohydrates)
(Stenberg et al., 2010; Viscarra-Rossel et al., 2009). Several important
spectral bands coincided with the clay spectral signatures (i.e., O–H
and metal-OH bends) were also identified, including spectral bands in
the region near 1400, 1900, and 2200 nm (smectites or illites) (Sor­
iano-Disla et al., 2014). Clays may form organo-mineral complexes with
soil organic materials that is important to protect soil organic carbon
from leaching and decomposition (Churchman, 2018; Lal et al., 2015;
McLauchlan, 2006).
The PLSRmod model for N predictions (Fig. 12) identified several
important spectral bands that coincided with nitrogen vibrational bond
spectral signatures (i.e., N–H, RC(O)NH2), particularly in the region
near 750 and 1500 nm (amine), and 1525 and 2030 nm (amides)
(Stenberg et al., 2010; Viscarra-Rossel et al., 2009). Several important

12
S.H. Adi et al.
spectral bands related to carbon vibrational bond signatures were also
observed along with the nitrogen-related molecule spectral signatures.
This co-existence is an evidence of the significant correlation between
organic carbon and nitrogen in East Java agricultural soils (Table 3).
Stenberg et al. (2010) argued that the important VNIR spectral bands for
N prediction could be dominated by carbon vibrational bond signatures,
possibly due to the soil organic matter (i.e., containing about 58% of
SOC) as the major source of organic nitrogen, the naturally dominant
form of carbon-nitrogen compounds in soils, and the lower concentra­
tion of N compared to SOC. The PLSRmod model for N prediction also
identified clay spectral signatures (i.e., 1400, 1900, and 2200 nm
wavelength) as the important N predictors (Fig. 12).
The important VNIR bands for pH, SB, and CEC predictions were
dominated by clay spectral signatures (metal-OH groups; Fig. 13Fig. 14
to Fig. 15) at the wavelength regions near 1400, 1900, 2200, and 2300
nm, that are possibly smectites, illites, or montmorillonites (Demattê
and da Silva Terra, 2014; Soriano-Disla et al., 2014). Soil pH,
exchangeable bases (i.e., SB), and CEC do not have active spectral sig­
natures in the VNIR region. The prediction of these soil properties are
depended on other VNIR-detectable soil attributes correlated with pH,
exchangeable bases, and CEC, such as clay (Stenberg et al., 2010; Terra
et al., 2015). Clay is important to pH, exchangeable bases, and CEC due
to the presence of negative charges on clay surfaces that interact reac­
tively with hydrogen ions (i.e., pH) and exchangeable cations (i.e., SB),
and on determining the capacity of soils to hold exchangeable cations (i.
e., CEC) (Murphy, 2015).
4. Conclusions
This research has demonstrated that acceptable spectroscopy models
were attainable for agricultural soil property predictions (i.e., SOC, N,
pH, SB, and CEC) in East Java, Indonesia. The utilization of the inte­
grative 2Step-R method offers the inclusion of important auxiliary pre­
dictor parameters (e.g., depth of sample, soil order, landform, and
parent materials) that provided additional information that were not
captured by the soil VNIR spectral data to predict soil properties. The
fused soil-environmental and VNIR spectral data showed to markedly
improve standard chemometric model performances compared to those
that solely use the VNIR spectra predictor dataset (i.e., standard PLSR),
specifically for soil N, pH, and SB predictions. The models also suc­
cessfully identified the important soil-environmental parameters and
VNIR bands that characterized the East Java agricultural soil properties.
This research has further demonstrated a promising application of
soil modeling as a cost-effective alternative method to conventional wet-
chemistry laboratory analysis. Limited soil data availability is the main
obstacle of agricultural land management in Indonesia. Soil data ac­
quisitions in this region is suboptimal due to the disparity between
allocated resources and the area to be monitored. Therefore, soil
modeling is poised to enhance soil monitoring programs in Indonesia.
Declaration of Competing Interests
The authors declare that they have no known competing financial
interests or personal relationships that could have appeared to influence
the work reported in this paper.
References
Adhikari, K., Hartemink, A.E., 2016. Linking soils to ecosystem services—a global
review. Geoderma 262, 101–111. https://doi.org/10.1016/j.
geoderma.2015.08.009.
Adi, S.H., Grunwald, S., 2020. Integrative environmental modeling of soil carbon
fractions based on a new latent variable model approach. Sci. Total Environ. 711,
134566 https://doi.org/10.1016/j.scitotenv.2019.134566.
American Society of Agronomy, Soil Science Society of America, 1982. Methods of soil
analysis, in: Page et al. (Eds.) Chemical and Microbiological Properties. Madison,
Wisconsin, USA, p. 1159.
13
Soil Security 5 (2021) 100025
Bellon-Maurel, V., Fernandez-Ahumada, E., Palagos, B., Roger, J.-.M., McBratney, A.,
2010. Critical review of chemometric indicators commonly used for assessing the
quality of the prediction of soil attributes by NIR spectroscopy. TrAC Trends Anal.
Chem. 29, 1073–1081. https://doi.org/10.1016/j.trac.2010.05.006.
Bellon-Maurel, V., McBratney, A., 2011. Near-infrared (NIR) and mid-infrared (MIR)
spectroscopic techniques for assessing the amount of carbon stock in soils–Critical
review and research perspectives. Soil Biol. Biochem. 43, 1398–1410. https://doi.
org/10.1016/j.soilbio.2011.02.019.
Bhattacharya, A., Dunson, D.B., 2011. Sparse Bayesian infinite factor models. Biometrika
19, 291–306. https://doi.org/10.1093/biomet/asr013.
Black, C., 1965. Method of soil analysis part 2. Chem. Microbiol. Prop. 9, 1387–1388.
Bouma, J., McBratney, A., 2013. Framing soils as an actor when dealing with wicked
environmental problems. Geoderma 200, 130–139. https://doi.org/10.1016/j.
geoderma.2013.02.011.
Brenning, A., 2008. Statistical geocomputing combining R and SAGA: the example of
landslide susceptibility analysis with generalized additive models. In: Böhner, J.,
Blaschke, T., Montanarella, L. (Eds.), SAGA — Seconds Out. Hamburger Beiträge Zur
Physischen Geographie Und Landschaftsökologie, pp. 23–32.
Chang, C.-.W., Laird, D.A., Mausbach, M.J., Hurburgh, C.R., 2001. Near-infrared
reflectance spectroscopy–principal components regression analyses of soil
properties. Soil Sci. Soc. Am. J. 65, 480–490. https://doi.org/10.2136/
sssaj2001.652480x.
Churchman, G.J., 2018. Game Changer in Soil Science. Functional role of clay minerals
in soil. J. Plant Nutr. Soil Sci. 181, 99–103. https://doi.org/10.1002/
jpln.201700605.
De, Jong, S., 1993. SIMPLS: an alternative approach to partial least squares regression.
Chemom. Intell. Lab. Syst. 18, 251–263. https://doi.org/10.1016/0169-7439(93)
85002-X.
Demattê, J.A., da Silva .F., Terra, 2014. Spectral pedology: a new perspective on
evaluation of soils along pedogenetic alterations. Geoderma 217, 190–200.
Dotto, A.C., Dalmolin, R.S.D., Grunwald, S., ten Caten, A., Pereira Filho, W., 2017. Two
preprocessing techniques to reduce model covariables in soil property predictions by
Vis-NIR spectroscopy. Soil Tillage Res 172, 59–68.
Dotto, A.C., Dalmolin, R.S.D., ten Caten, A., Grunwald, S., 2018. A systematic study on
the application of scatter-corrective and spectral-derivative preprocessing for
multivariate prediction of soil organic carbon by Vis-NIR spectra. Geoderma 314,
262–274. https://doi.org/10.1016/j.geoderma.2017.11.006.
Field, D.J., 2017. Soil Security: Dimensions, in: Global Soil Security. Springer, pp. 15–23.
Franklin, J., 2010. Mapping Species distributions: Spatial Inference and prediction,
Ecology, Biodiversity and Conservation. Cambridge University Press, New York.
Friedman, J., Hastie, T., Tibshirani, R., 2010. Regularization paths for generalized linear
models via coordinate descent. J. Stat. Softw. 33, 1–24.
Gray, J.M., Bishop, T.F., Wilson, B.R., 2015. Factors controlling soil organic carbon
stocks with depth in eastern Australia. Soil Sci. Soc. Am. J. 79, 1741–1751.
Gredilla, A., de Vallejuelo, S.F.-O., Elejoste, N., de Diego, A., Madariaga, J.M., 2016.
Non-destructive Spectroscopy combined with chemometrics as a tool for Green
Chemical Analysis of environmental samples: a review. TrAC Trends Anal. Chem. 76,
30–39.
Grunwald, S., Clingensmith, C.M., Gavilan, C.P., Mizuta, K., Wilcox, R.K.K., Pinheiro, É.
F., Ceddia, M.B., Ross, C.W., 2017. Integrating New Perspectives to Address Global
Soil security: Ideas from Integral Ecology. Global Soil Security. Springer,
pp. 319–329.
Grunwald, S., Thompson, J.A., Boettinger, J.L., 2011. Digital soil mapping and modeling
at continental scales: finding solutions for global issues. Soil Sci. Soc. Am. J. 75,
1201–1213. https://doi.org/10.2136/sssaj2011.0025.
Grunwald, S., Vasques, G., Rivero, R.G., 2015. Fusion of soil and remote sensing data to
model soil properties. In: Sparks, D.L. (Ed.), Advances in Agronomy, pp. 1–109.
Hartmann, J., Moosdorf, N., 2012. The new global lithological map database GLiM: a
representation of rock properties at the Earth surface. Geochem. Geophys.
Geosystems 13, 1–37. https://doi.org/10.1029/2012GC004370.
Helling, C.S., Chesters, G., Corey, R., 1964. Contribution of Organic Matter and Clay to
Soil Cation-Exchange Capacity as Affected by the pH of the Saturating Solution 1.
Soil Sci. Soc. Am. J. 28, 517–520.
Hijmans, R.J., 2016. raster: geographic Data Analysis and Modeling.
Hikmatullah, Tafakresnanto, Chendy, Sulaeman, Yiyi, 2016. Framing the Land Resources
Geospatial Information to Support Agricultural Area Development - Penyusunan
Informasi Geospasial Mendukung Pengembangan Kawasan Pertanian (No. 24/LA/
BBSDLP/2016). Indonesian Center for Agricultural Land Resources Research and
Development (ICALRRD), Bogor, Indonesia.
Hoerl, A., 1962. Application of ridge analysis to regression problems. Chem. Eng. Prog.
58, 54–59.
Hoerl, A.E., Kennard, R.W., 1970. Ridge regression: biased estimation for nonorthogonal
problems. Technometrics 12, 55–67. https://doi.org/10.1080/
00401706.1970.10488634.
Indonesia Center for Agricultural Land Resources Research and Development, 2009. Map
of Java Paddy-Rice Fields - Peta Lahan Sawah Jawa.
Indonesia Center for Agricultural Land Resources Research and Development, 2000. Map
of Indonesia Land System.
Indonesia Statistics Agency, 2016. East Java Climate [WWW Document]. Stat. East Java.
URL. https://jatim.bps.go.id/subject/151/iklim.html#subjekViewTab4 (accessed
9.17.08).
Islam, K., Singh, B., McBratney, A., 2003. Simultaneous estimation of several soil
properties by ultra-violet, visible, and near-infrared reflectance spectroscopy. Soil
Res 41, 1101–1114.
Jarvis, A., Reuter, H.I., Nelson, A., Guevara, E., 2008. Hole-filled SRTM for the globe
Version 4, available from the CGIAR-CSI SRTM 90 m Database.
S.H. Adi et al.
Knox, N.M., Grunwald, S., McDowell, M.L., Bruland, G.L., Myers, D.B., Harris, W.G.,
2015. Modelling soil carbon fractions with visible near-infrared (VNIR) and mid-
infrared (MIR) spectroscopy. Geoderma 239, 229–239. https://doi.org/10.1016/j.
geoderma.2014.10.019.
Koch, A., McBratney, A., Adams, M., Field, D., Hill, R., Crawford, J., Minasny, B., Lal, R.,
Abbott, L., O’Donnell, A., others, 2013. Soil security: solving the global soil crisis.
Glob. Policy 4, 434–441.
Kottek, M., Grieser, J., Beck, C., Rudolf, B., Rubel, F., 2006. World map of the Köppen-
Geiger climate classification updated. Meteorol. Z. 15, 259–263. https://doi.org/
10.1127/0941-2948/2006/0130.
Kusumo, B., Sukartono, S., Bustan, B., 2018a. The rapid measurement of soil carbon stock
using near-infrared technology. In: IOP Conference Series: Earth and Environmental
Science. IOP Publishing, pp. 1–7. https://doi.org/10.1088/1755-1315/129/1/
012023.
Kusumo, B., Sukartono, S., Bustan, B., 2018b. Rapid Measurement of Soil Carbon in Rice
Paddy Field of Lombok Island Indonesia Using Near Infrared Technology. In: IOP
Conference Series: Materials Science and Engineering. IOP Publishing, pp. 1–7.
https://doi.org/10.1088/1757-899X/306/1/012014.
Lal, R., 2010. Managing soils and ecosystems for mitigating anthropogenic carbon
emissions and advancing global food security. Bioscience 60, 708–721.
Lal, R., 2006. Enhancing crop yields in the developing countries through restoration of
the soil organic carbon pool in agricultural lands. Land Degrad. Dev. 17, 197–209.
https://doi.org/10.1002/ldr.696.
Lal, R., 2004. Soil carbon sequestration impacts on global climate change and food
security. Science 304, 1623–1627. https://doi.org/10.1126/science.1097396.
Lal, R., Negassa, W., Lorenz, K., 2015. Carbon sequestration in soil. Curr. Opin. Environ.
Sustain. 15, 79–86. https://doi.org/10.1016/j.cosust.2015.09.002.
Lowe, D.J., Tonkin, P.J., 2010. Unravelling upbuilding pedogenesis in tephra and loess
sequences in New Zealand using tephrochronology. In: Proceeding of the 19th World
Congress of Soil Science, Soil Solutions for a Changing World. IUSS, Brisbane,
Australia, pp. 33–34.
McBratney, A., Field, D.J., Koch, A., 2014. The dimensions of soil security. Geoderma
213, 203–213 https://doi.org/10/gkxvgk.
McBratney, A.B., Santos, M.M., Minasny, B., 2003. On digital soil mapping. Geoderma
117, 3–52. https://doi.org/10.1016/S0016-7061(03)00223-4.
McLauchlan, K.K., 2006. Effects of soil texture on soil carbon and nitrogen dynamics
after cessation of agriculture. Geoderma 136, 289–299.
Mevik, B.-.H., Wehrens, R., 2018. Introduction to the pls Package.
Mizuta, K., Grunwald, S., Phillips, M.A., 2018. A new soil index development and
integration with econometric theory. Soil Sci. Soc. Am. J. 82, 1017–1032. https://
doi.org/10.2136/sssaj2017.11.0378.
14
Soil Security 5 (2021) 100025
Murphy, B.W., 2015. Impact of soil organic matter on soil properties—A review with
emphasis on Australian soils. Soil Res 53, 605–635. https://doi.org/10.1071/
SR14246.
Pinheiro, É.F., Ceddia, M.B., Clingensmith, C.M., Grunwald, S., Vasques, G.M., 2017.
Prediction of Soil Physical and Chemical Properties by Visible and Near-Infrared
Diffuse Reflectance Spectroscopy in the Central Amazon. Remote Sens 9, 1–22.
Core Team, R., 2017. R: A Language and Environment for Statistical Computing. R
Foundation for Statistical Computing, Vienna, Austria.
Savitzky, A., Golay, M.J., 1964. Smoothing and differentiation of data by simplified least
squares procedures. Anal. Chem. 36, 1627–1639.
Sigit, S., 1965. Geologic map of Indonesia - Peta geologi Indonesia (Report No. 414).
IMAP. https://doi.org/10.3133/i414.
Signal Developers, 2014. signal: Signal processing.
Smith, P., House, J.I., Bustamante, M., Sobocká, J., Harper, R., Pan, G., West, P.C.,
Clark, J.M., Adhya, T., Rumpel, C., Paustian, K., Kuikman, P., Cotrufo, M.F.,
Elliott, J.A., Mcdowell, R., Griffiths, R.I., Asakawa, S., Bondeau, A., Jain, A.K.,
Meersmans, J., Pugh, T.A.M., 2016. Global change pressures on soils from land use
and management. Glob. Change Biol 22, 1008–1028.
Soriano-Disla, J.M., Janik, L.J., Viscarra-Rossel, R.A., Macdonald, L.M., McLaughlin, M.
J., 2014. The performance of visible, near-, and mid-infrared reflectance
spectroscopy for prediction of soil physical, chemical, and biological properties.
Appl. Spectrosc. Rev. 49, 139–186.
Stenberg, B., Viscarra-Rossel, R.A., Mouazen, A.M., Wetterlind, J., 2010. Visible and near
infrared spectroscopy in soil science. Adv. Agron. 107, 163–215.
Tanikawa, T., Hashimoto, Y., Yamaguchi, N., Ito, Y., Fukushima, S., Kanda, K.,
Uemura, M., Hasegawa, T., Takahashi, M., Yoshinaga, S., 2014. Sulfur accumulation
in Melanudands during development by upbuilding pedogenesis since 14–15 cal. ka.
Geoderma 232, 609–618.
Terra, F.S., Demattê, J.A.M., Viscarra-Rossel, R.A., 2015. Spectral libraries for
quantitative analyses of tropical Brazilian soils: comparing vis–NIR and mid-IR
reflectance data. Geoderma 255, 81–93.
Viscarra-Rossel, R.A., Cattle, S.R., Ortega, A., Fouad, Y., 2009. In situ measurements of
soil colour, mineral composition and clay content by vis–NIR spectroscopy.
Geoderma 150, 253–266.
Wehrens, R., Mevik, B., 2007. The pls package: principal component and partial least
squares regression in R. J. Stat. Softw. 18, 1–23. https://doi.org/10.18637/jss.v018.
i02.
Xiong, X., Grunwald, S., Myers, D.B., Kim, J., Harris, W.G., Comerford, N.B., 2014.
Holistic environmental soil-landscape modeling of soil organic carbon. Environ.
Model. Softw. 57, 202–215. https://doi.org/10.1016/j.envsoft.2014.03.004.