Computers and Electronics in Agriculture 177 (2020) 105710

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Computers and Electronics in Agriculture

journal homepage: www.elsevier.com/locate/compag

Use of color parameters in the grouping of soil samples produces more T

accurate predictions of soil texture and soil organic carbon
⁎
José Janderson Ferreira Costaa, , Élvio Giassona, Elisângela Benedet da Silvab,
João Augusto Coblinskia, Tales Tiechera
a
Department of Soil Science, School of Agronomy, Federal University of Rio Grande do Sul State, Bento Gonçalves Avenue 7712, 91540-000 Porto Alegre, Brazil
b
Agricultural Research and Rural Extension Corporation of Santa Catarina, Rodovia Admar Gonzaga 1347, 88034-901 Florianópolis, Santa Catarina, Brazil

A R T I C LE I N FO A B S T R A C T

Keywords: Prediction of soil properties such as texture and soil organic carbon (SOC) content by reflectance spectroscopy
Reflectance spectroscopy (RS) is influenced by the heterogeneity of soil samples used to calibrate multivariate models. These soil prop-
Soil organic carbon erties are directly related to color, which, in turn, can be estimated by color parameters derived from the visible
Soil texture (Vis) spectrum at no additional cost. At present, only a few publications have addressed the effect that input data
Color parameters
structure and soil heterogeneity have on model performance. Therefore, the objectives of this study were to use
Multivariate calibration models
Vis-based-color parameters combined with multivariate statistical techniques to group soil samples and com-
paring the results of different SOC, clay, sand and silt prediction models. Soil sampling was conducted over an
area of approximately 500 ha in the region of São Joaquim National Park, Santa Catarina State, Brazil, where a
total of 260 soil samples were collected. Soil reflectance data were obtained by Vis-NIR-SWIR spectroscopy in the
laboratory, through a spectroradiometer that covers the 350–2500 nm. Soil organic carbon content was de-
termined by dry combustion in an elemental analyzer. Sand, silt and clay fractions were determined using the
pipette method. Twenty-two components of color parameters were derived from the Vis spectrum with the use of
colorimetry models. For the definition of the most appropriate number of soil sample clusters, two multivariate
statistical analyzes: principal component analysis (PCA) and cluster analysis of the samples were applied to the
color parameter values. Partial least squares regression (PLSR) and support vector machines (SVM) multivariate
models were calibrated for each cluster and also for the models without stratification using 260 soil samples and
95 selected samples (MWS-260 and MWS-95). Overall, the PLSR model performed better than the SVM model, as
confirmed by the statistical difference between RMSE results. Multivariate statistical analyzes applied to color
parameters were able to group soil samples with similar characteristics, reducing data amplitude and improving
the accuracy of soil property predictions. These analyzes demonstrated that the use of Vis-based-color para-
meters to group soil samples can be a quick and inexpensive way to increase the potential of spectroscopy to
accurately predict soil physical and chemical properties.

1. Introduction
Understanding the spatial variability of soil properties may improve
management and conservation strategies, as well as conscious use of
soil resources (Gholizadeh et al., 2018). More data on the spatial
variability of soil properties is necessary to support the development
and implementation of management strategies (Nocita et al., 2014;
Viscarra Rossel et al., 2016). However, due to the high costs of la-
boratory chemical analysis, this practice has not yet become econom-
ically viable (Nanni et al., 2011).
Remote and proximal sensing techniques have been proposed as
efficient methods to study soil properties. Among these methods, re-
flectance spectroscopy (RS) in the visible, near and shortwave infrared
(Vis-NIR-SWIR) regions (350–2500 nm) is a technique capable of
measuring various soil properties at a low cost (O’Rourke and Holden,
2011). Reflectance spectroscopy is a technique widely used in soil
analysis laboratories that has recently also increased its field applica-
tion. Soil spectral signatures allow inferring information about soil
physical, chemical and mineralogical composition, and such inference
is based on multivariate calibration models developed from spectral
libraries that correlate reflectance spectra with laboratory-measured
soil property data (Gupta et al., 2018; Pabón et al., 2019; Stevens et al.,

⁎
Corresponding author at: Federal University of Rio Grande do Sul State, Brazil.
E-mail address: janderson.ferreirac@gmail.com (J.J.F. Costa).

https://doi.org/10.1016/j.compag.2020.105710
Received 6 May 2020; Received in revised form 4 August 2020; Accepted 9 August 2020
Available online 20 August 2020
0168-1699/ © 2020 Elsevier B.V. All rights reserved.
J.J.F. Costa, et al.
2013).
Due to the wide variation in the mineralogical composition and
physical and chemical properties of soils, many studies have used
spectral samples and libraries that represent the variability of soils, as
follows: at local scale (Dotto et al., 2016; Gholizadeh et al., 2016; Silva
et al., 2016); at regional scale (Franceschini et al., 2013; Ramirez-Lopez
et al., 2013); at national scale (Araújo et al., 2014; Shi et al., 2014;
Viscarra Rossel and Chen, 2011); at continental scale (Nocita et al.,
2014; Stevens and Ramirez Lopez, 2014), and at global scale (Ramirez-
Lopez et al., 2013; Viscarra Rossel et al., 2016). Other studies re-
commend an adaptation of the models according to the characteristics
of the local samples, called “spiking” samples (Guerrero et al., 2014,
2010; Zhao et al., 2018), where representative local samples of the
study area are inserted in spectral libraries on a regional scale. The
development of these libraries with a large number of samples is in-
tended to ensure that local samples fall within the domain of the model
(Grinand et al., 2012; Viscarra Rossel and Webster, 2012). However,
there is no certainty because soils have highly variable features, even at
a regional scale, making assessment more difficult, impacting model
performance (Stenberg et al., 2010; Viscarra Rossel et al., 2016).
To improve model performance, many studies have used different
types of pre-processing techniques and multivariate models (Table 1).
Allo et al. (2020), on a local scale, with 95 samples, applied the PLSR
algorithm and three pre-processing techniques to a data set with soil
organic carbon (SOC) content ranging from 0.4 to 13% and found that
the best performance was obtained with the use of a combination of
pre-processing techniques (DET + FDSG). Allory et al. (2019) observed
a better predictive capacity using a combination of pre-processing
techniques (SG + SNV) that showed better performance when only one
pre-processing technique was used. Likewise, Dotto et al. (2017), on a
local scale, with 299 soil samples and clay content ranging from 21 to
78% and sand ranging from 1 to 35%, obtained R2 of 0.62 and RMSE of
6.8% for clay and R2 of 0.25 and RMSE of 6.4% for sand, using the SVM
algorithm and the DET pre-processing technique.
However, the prediction results obtained by Demattê et al. (2016),
on a different scale, showed differences in the performance of SOC
content models and sand, clay and silt fractions, which may have been
influenced by the number of samples in the calibration data set. This
demonstrates that the input data structure is a factor that also influ-
ences the predictive capacity of the models.
At present, only a few publications have addressed the effect that
input data structure and soil heterogeneity have on model performance.
Jiang et al. (2017) collected soil samples in surface (0–0.1 m) and
subsurface (0.1–0.3 m) layers in central China and identified differ-
ences in the variability of SOC levels for each soil depth, which affected
the performance of prediction models. Araújo et al. (2014) by segre-
gating data from a spectral library of soil into more homogeneous
groups in relation to the mineralogy of the clay fraction, obtained a
reduction of 21% in the prediction error of that fraction. Moura-Bueno
et al. (2019) found that segregating samples based on soil classes, uses
and layers, improved the accuracy of multivariate models in the pre-
diction of soil carbon. However, one possibility that can still be ex-
plored is the establishment of a criterion for grouping samples based on
soil color and dividing them into homogeneous groups according to soil
features. There are many known relationships between soil color and its
mineralogical, physical and chemical characteristics (Aitkenhead et al.,
2013b, 2013a; Ben-Dor et al., 1997; Davey et al., 1975; Murti and
Satyanarayana, 1971; Viscarra Rossel et al., 2009; Vodyanitskii and
Savichev, 2017). Examples of variations in soil color associated with
soil properties include dark color of organic matter (OM), white color of
quartz, calcite and other carbonates, red color of hematite (α-Fe2O3)
and yellow color of goethite (α- FeOOH) (Aitkenhead et al., 2013b,
2013a). Thus, previous clustering of soils by color may favor modeling,
providing prediction models with subgroups with less variability of
organic matter, quartz, iron oxides or other elements.
The easiest and fastest way to measure or characterize soil color is
2
Computers and Electronics in Agriculture 177 (2020) 105710
through the Munsell Color System (Munsell Soil Color Charts, 2000)
which classifies colors into three components: hue, value, and chroma,
where hue is the dominant spectral color; value indicates the degree of
lightness or darkness of a color, and chroma is the purity or strength of
the spectral color (Soil Survey Division Staff, 2017). However, more
recent approaches to color measurement include the use of computer-
coupled sensors such as colorimeters, spectrophotometers and spec-
troradiometers (Levin et al., 2005; Moreno-Ramón et al., 2014; Viscarra
Rossel et al., 2008). These devices record the energy reflected by the
soil, which absorbs certain wavelengths, and the combination of the
reflected wavelengths determines soil color (Schanda, 2007; Viscarra
Rossel et al., 2009). Thus, soil color can be derived from spectral curves
generated for previous studies at no additional cost and can be re-
presented by color space models.
So far, although color parameters have been applied in studies to
estimate soil color, mineral composition and clay content (Aitkenhead
et al., 2013a; Dominguez et al., 2010; Viscarra Rossel et al., 2009), in
the identification of SOC content (Vodyanitskii and Savichev, 2017),
and discrimination of sediment source (Martínez-Carreras et al., 2010a,
2010b; Tiecher et al., 2015), there is no attempt available in the lit-
erature using color parameters to stratify a set soil samples and group
them into homogeneous groups to predict soil properties. Mouazen
et al. (2007) evaluated soil color using Munsell chart for using in soil
classification. They used the parameters Hue, Value and Chroma to
characterize soil colors and PCA to discriminate samples. However,
color can be better represented when a larger number of parameters
representing color in different scales are used (Viscarra Rossel et al.,
2006). Therefore, the objectives of this study were to use Vis-based-
color parameters combined with multivariate statistical techniques to
group soil samples and comparing the results of different SOC, clay,
sand and silt prediction models.
2. Material and methods
2.1. Characterization of the study area
The study area is located in São Joaquim National Park (SJNP),
southern plateau region of the State of Santa Catarina (SC), Brazil
(Fig. 1). This Conservation Unit (CU) has an approximate area of
49,300 ha, with very rugged relief and altitudes ranging from 300 to
1826 m. The park is located in a cold region, and the average annual
temperature ranges from 12 °C to 14 °C (Vianna et al., 2015). It is the
only park in Brazil devoted to the conservation of Araucaria (Araucaria
angustifolia) and covers four main types of phytophysiognomy (Klein,
1978): Araucaria forest, subtropical forest, dwarf cloud forest or dwarf
cloud highland forest and campos gerais de altitude (natural highland
grasslands). The soils are mostly formed by volcanic and sedimentary
rocks of the Paraná Basin of the Serra Geral group (Serra Geral, Palmas,
Paranapanema, Gramado and Botucatu formation) and the Passa Dois
group (Rio do Rastro and Teresina formation) (Embrapa, 2004; Wildner
et al., 2014). The volcanic rocks of Serra Geral formation are dominant
and characterized by basalts and andesites (basic) and rhyolites and
riodacites (acidic). The soils in this region usually have a humic or
prominent A horizons (Dalmolin et al., 2017; Embrapa, 2004), with
very high exchangeable Al contents and high potential acidity, low sum
of base cations and base saturation, and with an accentuated undulating
relief. These soils are moderately shallow and can be classified as En-
tisols and Inceptisols (Dalmolin et al., 2017; Embrapa, 2004).
Research modules of the Biodiversity Research Program, Atlantic
Forest, Santa Catarina (PPBio-MA-SC) were installed in this area. The
module area has 500 ha (1 × 5 km) and is composed of two east-west
accesses. Inside module, 20 plots were installed: 10 terrestrial (Fig. 1)
and 10 riparian plots. The plots are 250 m corridors along the contour
lines and are demarcated by 6 pickets, one every 50 m (0, 50, 100, 150,
200 and 250 m). A total of 260 soil samples were collected using two
sampling systems. In the first sampling system 145 soil samples were
J.J.F. Costa, et al. Computers and Electronics in Agriculture 177 (2020) 105710

Table 1
Selection of studies that applied different types of pre-processing and multivariate models to estimate SOC, sand, silt and clay contents using spectroscopy.
b a
Scale M. method S. pre-processing Samples SOC Clay Sand Silt Source

R2v RMSE% R2v RMSE% R2v RMSE% R2v RMSE%

Local PLSR PCA 144 0.84 0.1 0.78 3.9 0.79 3.4 0.65 2.6 (Margenot et al., 2020)
Local PLSR - 95 0.92 0.8 n.a. n.a. n.a. n.a. n.a. n.a. (Allo et al., 2020)
Local PLSR DET + FDSG 95 0.94 0.7 n.a. n.a. n.a. n.a. n.a. n.a. (Allo et al., 2020)
Local PLSR SNV + FDSG 95 0.92 0.8 n.a. n.a. n.a. n.a. n.a. n.a. (Allo et al., 2020)
Local PLSR SG 186 0.40 1.0 n.a. n.a. n.a. n.a. n.a. n.a. (Allory et al., 2019)
Local PLSR SG + SNV 186 0.83 0.5 n.a. n.a. n.a. n.a. n.a. n.a. (Allory et al., 2019)
Local PLSR SG + FDSG 186 0.83 0.5 n.a. n.a. n.a. n.a. n.a. n.a. (Allory et al., 2019)
Local PLSR SG + SDSG 186 0.82 0.5 n.a. n.a. n.a. n.a. n.a. n.a. (Allory et al., 2019)
National Cubist CRR 39,284 n.a. n.a. 0.88 7.6 0.87 10.3 n.a. n.a. (Demattê et al., 2019)
Local PLSR MSC 90 0.66 0.2 n.a. n.a. n.a. n.a. n.a. n.a. (Hutengs et al., 2019)
Regional PLSR SG 1013 n.a. n.a. 0.73 5.4 0.72 9.2 0.59 5.9 (Vasava et al., 2019)
National PLSR SNV, SG 10,802 n.a. n.a. 0.97 1.9 0.96 6.6 0.94 5.6 (Jaconi et al., 2019)
Local PLSR SG 148 0.74 0.2 n.a. n.a. n.a. n.a. n.a. n.a. (Nawar and Mouazen, 2018)
Regional PLSR SG 591 0.80 0.1 0.58 6.2 0.67 7.8 0.70 7.8 (Xu et al., 2018)
Local SVM DET 299 0.86 0.4 0.62 6.8 0.25 6.4 0.50 6.2 (Dotto et al., 2017)
Local SVM CRR 299 0.86 0.4 0.58 7.2 0.25 6.3 0.50 6.2 (Dotto et al., 2017)
Local PLSR CRR 299 0.83 0.4 0.52 7.5 0.17 6.5 0.56 5.3 (Dotto et al., 2017)
Local PLSR CRR + BR 299 0.79 0.5 0.45 8.3 0.18 6.5 0.44 6.7 (Dotto et al., 2017)
Local PLSR DET 299 0.72 0.5 0.40 8.8 0.19 6.5 0.44 6.7 (Dotto et al., 2017)
Local SVR FDSG 300 n.a. n.a. 0.53 7.9 0.18 5.5 0.39 9.1 (Duda et al., 2017)
Local PCR – 216 0.69 0.9 n.a. n.a. n.a. n.a. n.a. n.a. (Lucà et al., 2017)
Local PLSR SNV 216 0.79 0.7 n.a. n.a. n.a. n.a. n.a. n.a. (Lucà et al., 2017)
Local SVM – 216 0.82 0.7 n.a. n.a. n.a. n.a. n.a. n.a. (Lucà et al., 2017)
Local PLSR MSC, FDSG 200 n.a. n.a. 0.78 6.9 0.82 6.7 0.42 2.1 (Nanni et al., 2017)
Local PLSR SG/SNV 434 0.71 0.6 0.78 6.2 0.62 11.5 0.36 9.5 (Pinheiro et al., 2017)
Local Cubist SDSG/SNV 257 n.a. n.a. 0.70 14.7 0.50 18.3 0.00 16.7 (Zhang et al., 2017)
Regional PLSR PCA 7185 0.63 0.3 0.85 9.8 0.86 10.2 0.51 3.8 (Demattê et al., 2016)
Regional PLSR PCA 903 0.65 0.3 0.77 10.4 0.78 11.8 0.55 3.3 (Demattê et al., 2016)
Regional PLSR PCA 3093 0.61 0.2 0.67 3.2 0.64 4.2 0.30 2.6 (Demattê et al., 2016)
Local PLSR PCA 621 0.62 0.2 0.77 7.3 0.77 7.3 0.21 1.4 (Demattê et al., 2016)
Local PLSR PCA 563 0.54 0.3 0.74 11.3 0.77 12.7 0.71 3.1 (Demattê et al., 2016)
Local PLSR PCA 843 0.66 0.1 0.71 2.8 0.68 3.8 0.21 3.0 (Demattê et al., 2016)
Local PLSR PCA 541 0.61 0.4 0.55 7.6 0.45 6.7 0.50 3.8 (Demattê et al., 2016)
Global Cubist CRR 23,631 0.92 1.1 0.80 10.3 0.68 18.8 0.79 10.3 (Viscarra Rossel et al., 2016)
Local PLSR SNV 306 n.a. n.a. 0.78 3.1 n.a. n.a. n.a. n.a. (Camargo et al., 2015)
Regional PLSR SDSG 7172 0.60 0.6 0.82 10.9 n.a. n.a. n.a. n.a. (Araújo et al., 2014)
Regional SVM SDSG 7172 0.69 0.5 0.89 8.9 n.a. n.a. n.a. n.a. (Araújo et al., 2014)
Local PLSR SVN, SG, MSC 129 n.a. n.a. 0.92 5.2 0.87 7.3 0.80 3.1 (Franceschini et al., 2013)
Regional PLSR RAW 129 0.65 0.4 n.a. n.a. n.a. n.a. n.a. n.a. (Cambule et al., 2012)
Regional PLSR RAW-FDSG 129 0.85 0.3 n.a. n.a. n.a. n.a. n.a. n.a. (Cambule et al., 2012)
Regional PLSR SGD-FDSG 129 0.81 0.3 n.a. n.a. n.a. n.a. n.a. n.a. (Cambule et al., 2012)
Regional PLSR MSC 129 0.75 0.3 n.a. n.a. n.a. n.a. n.a. n.a. (Cambule et al., 2012)
Regional PLSR MSC – SGD 129 0.77 0.3 n.a. n.a. n.a. n.a. n.a. n.a. (Cambule et al., 2012)
Regional PLSR SNV 129 0.73 0.4 n.a. n.a. n.a. n.a. n.a. n.a. (Cambule et al., 2012)
Regional PLSR MSC – FDSG 129 0.78 0.3 n.a. n.a. n.a. n.a. n.a. n.a. (Cambule et al., 2012)
Regional PLSR MSC – FDSG 129 0.84 0.3 n.a. n.a. n.a. n.a. n.a. n.a. (Cambule et al., 2012)
Local PLSR SNV 148 n.a. n.a. 0.74 12.0 0.56 24.0 0.46 49.0 (Vendrame et al., 2012)
Global BTR SMO, FDSG 3793 0.82 0.9 0.73 9.5 n.a. n.a. n.a. n.a. (Brown et al., 2006)

a
PLSR: partial least squares regression; SVM: support vector machine; GPR: Gaussian process regression; RF: random forest; MARS: multivariate adaptive re-
gression splines; BTR: boosted regression trees; BR: band ratio; CRR: continuum removal; MSC: multiplicative scatter-correction; DET: detrend; SDSG: Savitzky–Golay
second derivative; FDSG: Savitzky–Golay first derivative; SNV: standard normal variate; PCA: principal component analysis; DER: derivative; R2v: coefficient of
determination; RMSEv: root mean square error of validation; n.a.: Not available.
b
The criterion for differentiating at the scale of the spectral library is usually the spatial coverage and the number of soil samples.

collected (in terrestrial plots) using the PPBio protocol, with adaptation
in the collection depth according to GlobalSoilMap.Net (0–10, 10–20,
20–30 and 30–60 cm depth). In the second sampling system 115 soil
samples were collected (outside the plots, in different locations of the
module), using the conditioned Latin Hypercube Sampling (cLHs) ap-
proach (Minasny and McBratney, 2006). This sampling used a set of
continuous or categorical environmental covariables that represent the
“predictor space” in which the most representative landscape sites were
selected.
A set of environmental covariables were selected to compose the
predictor space of the module based on the methodology proposed by
Stumpf et al. (2016), with adaptations. The selection was based on the
lowest correlation (r < 0.4) between the environmental covariables to
avoid collinearity (Mulder et al., 2012). Another selection was then
made following the criterion of larger correlation (r greater than 0.4)
between the covariables selected in the previous step and the SOC
content obtained by soil analysis of the samples collected in terrestrial
plots. Thus, two variables with higher and lower r were selected,
namely altitude and slope.
2.2. Spectral reflectance measurements and laboratory analysis
Soil reflectance data were obtained by Vis-NIR-SWIR spectroscopy,
based on the absorption spectrum produced after the reading of the soil
samples with a spectral sensor. The spectral data ware obtained using a
FieldSpec 3 spectroradiometer (Analytical Spectral Devices, Boulder,
USA) with the ASD Contact Probe® set that covers the spectral range
350–2500 nm at 1 nm resolution. For spectra acquisition, the samples

3
J.J.F. Costa, et al.
Fig. 1. Research module and location of plots where soil samples were collected at São Joaquim. National Park, in Santa Catarina State, Brazil, with 95 soil collection
points.
were air-dried, ground and sieved (2 mm). The samples were placed in
petri dishes (7.5 cm in diameter and 2 cm in height) and their surface
was homogenized so that there was no interference in the readings. We
used a tripod that keeps the probe constant, moving the sample so that
there was contact with the Contact Probe. The sensor was calibrated at
the beginning of spectral measurements and every 20 min during
readings using a Spectralon white plate (Labsphere, North Sutton, NH,
USA) with more than 100% reflectance. Three readings were obtained
for each sample and the mean spectral curve was used for analysis. The
acquisition of spectra was obtained according to Ben Dor et al. (2015)
and Romero et al. (2018). To reduce interference in the spectra caused
by the soil-device-light source environment combination, the original
spectral curves were only smoothed using Savitzky-Golay filter (with
adjustment through second-order polygon and 1 nm search window).
For the determination of soil SOC contents, subsamples with ap-
proximately 3 g of soil were milled and sieved < 0.25 mm. The sub-
samples were stored in Eppendorf vials for dry combustion analysis in a
Flash 2000 Organic Elemental Analyzer (Zobeck et al., 2013). The
particle size fractions of clay, silt, and sand were determined using the
pipette method (Donagemma et al., 2017).
2.3. Vis-based-color parameters calculation
The methodological sequence applied in this study is shown in the
flow chart of Fig. 2. Twenty-two (22) components were derived from
the Vis spectrum using various colorimetry models described in detail
by Viscarra Rossel et al. (2006). The Commission Internationale de
l'Eclairage (CIE, 1996) proposed the CIE models to facilitate visualiza-
tion and to standardize color models. XYZ tristimulus values were
calculated based on the color-matching functions defined in 1931 by
the CIE (CIE, 1996), where Y represents the brightness and X and Z are
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Computers and Electronics in Agriculture 177 (2020) 105710
virtual components of the primary spectra. The derived XYZ values
were then transformed into nineteen other color space models (i.e.,
RGB, Munsell HVC, CIE xyY, CIE La*b*, CIE Lu*v*, CIE Lc*h*, and
CMYK chromaticity coordinates) using the Munsell Conversion soft-
ware (WallkillColor, 2019). In the CIE xyY system, Y represents lumi-
nance and x and y represent color variations from blue to red and blue
to green, respectively. In the CIE La*b* and CIE Lu*v* systems, L re-
presents brightness or luminance, and a* and b* and u* and v* re-
present chromaticity coordinates, as opponent red-green and blue-
yellow scales. CIE Lc*h* model represents a transformation of the CIE
La*b* spherical color space into cylindrical coordinates, resulting in
hue (h*) and chroma (c*) values. The RGB system forms a cube com-
prising red (R), green (G) and blue (B) orthogonal axes, from which
each color can be produced by a mixture of these three primary colors.
The CMYK model is an abbreviation of the system formed by the colors
Cyan, Magenta, Yellow and Black. The Munsell HVC system used in soil
science describes soil color using hue (H), value (V), and chroma (C).
Table 2 presents a summary of the color space models used in this study
and the abbreviations for all 22 calculated color parameters.
2.4. Descriptive and multivariate statistical analyzes
Descriptive statistics was performed for SOC contents and sand, silt
and clay fractions, showing a great variability of these properties,
especially for SOC contents (Table 3). Thus, criteria had to be estab-
lished for dividing the group of samples into subgroups. Two multi-
variate statistical analyzes were applied to the color parameter values:
Principal Component Analysis (PCA) and Cluster Analysis of the sam-
ples (or cluster), both performed on the R computing platform (R
Development Core Team, 2017).
J.J.F. Costa, et al.
Fig. 2. Methodological sequence of spectral reflectance measurements and laboratory analysis. In the sequence, the Vis-based-color parameters calculation, the
multivariate analysis and the construction of the prediction models. MWS-260: model without stratification using 260 soil samples; MWS-95: model without stra-
tification using 95 selected samples.
2.5. Principal component analysis (PCA)
Principal component analysis was applied to color parameter values
to reduce the dimensionality of such data in multivariate space and
visualize their distribution patterns and structures that allow them to
identify clusters and outliers (Galvãdo et al., 1995). Each principal
component is represented by an axis orthogonal to the other axes,
which is formed by a linear combination of the original variables. Ac-
cording to this technique, the distance preserved between the de-
scriptors was the Euclidean distance and the relationships identified are
linear (Borcard et al., 2011). The descriptors used in this study were the
color parameters: XYZ, RGB, Munsell HVC color coordinates, CIE xyY,
CIE La*b*, CIE Lu*v*, CIE Lc*h* and CMYK. As these variables are
measured in different units of measurement, the values had to be
converted to the same scale to equalize the statistical significance of all
5
Computers and Electronics in Agriculture 177 (2020) 105710
variables, thus simplifying mathematical relationships, as suggested by
Legendre and Legendre (1998). Then, the variables were linearly
transformed through a data translation and expansion process, by
subtracting a constant (mean) from each value and then dividing them
by another constant (standard deviation). This transformation is called
standardization or z-scores, and is often used in PCA. The scale function
of the base package was used to perform this transformation. PCA was
applied with the use of the princomp function of the stats package on
descriptor values to extract information from the 22 color parameters
across the entire sample set, on a single 260 × 22 matrix. Principal
component scores were used to determine the optimal number of
clusters in the subsequent step. A general implementation of PCA is
given by Eq. (1).
PC1 = (B1 .e1,1) + (B2 .e1,2) + ...+(Bn .e1,n)
J.J.F. Costa, et al. Computers and Electronics in Agriculture 177 (2020) 105710

Table 2 (color parameters); e is the eigenvector (contribution of each original

Vis-based-color parameters derived from different color space models and cal- data to the score), and n is the number of parameters.
culated using Munsell Conversion software (WallkillColor, 2019).
Color space Color parameters Parameter abbreviation 2.6. Cluster analysis of samples
template
For the stratification of the set of soil samples, Fuzzy K-means (FKM)
RGB Red R
Green G clustering was applied to the PCA scores, to discriminate different soil
Blue B samples based on color parameter values that were described in detail
CIE xyY Chromatic coordinate x x
by Terra et al. (2018). The most appropriate number of clusters and
Chromatic coordinate y y PCA scores for clustering were established by the following indices:
Brightness Y partition coefficient (PC) (Eq. (2)), partition entropy (PE) (Eq. (3)) and
CIE XYZ Virtual component X X modified partition coefficient (MPC) (Eq. (4)) (Ferraro and Giordani,
Virtual component Z Z 2015; Wu and Yang, 2005). Two (2) to 4 PCA scores and 2 to 8 clusters
CIE Luv Metric lightness function L were tested. According to the best PC and MPC score, it was defined
Chromatic coordinate opponent u* that the ideal number of clusters would be three. Therefore, the group
red-green scales of 260 soil samples was divided into three subgroups, as follows: the
Chromatic coordinate opponent v* first with 91 samples; the second with 95 samples and the third with 74
blue-yellow scales
samples. To facilitate understanding, the subgroups were considered as
CIE Lab Chromatic coordinate opponent a* clusters and the whole sample set containing all samples was con-
red-green scales
sidered as model without stratification (MWS-260). The model without
Chromatic coordinate opponent b*
blue-yellow scales stratification with 95 selected samples was considered as MWS-95.
CIE Lch CIE chroma c* k
1 n
CIE hue h* PC(k) =
n
∑j =1 ∑ u2ij
i=1 (2)
CMYK Cyan C
Magenta M where ≤ PC (k) ≤ 1. In general, we find an optimal cluster number
1
k
Yellow Ye
k* by solving max2⩽k⩽n−1PC(k) to produce a best clustering perfor-
Black K
mance for the data set; uij is the degree of membership of sample j.
Munsell HVC Hue Hue
k
Value Value 1 n
Chroma Chroma PE(k) = −
n
∑j =1 ∑ uijlog2uij
i=1 (3)
where 0 ≤ PE (k) ≤ log 2 k. In general, we find an optimal k* by solving
Table 3 min2⩽k⩽n−1PE(k) to produce a best clustering performance for the data
Descriptive statistics of soil properties and color parameters.
set.
Soil properties and Mean SD Minimum Maximum CV %
parameters
k
MPC(k) = 1 − (1 − PC(k))
k−1 (4)
SOC (%) 11.07 7.70 0.64 34.84 70
Clay (%) 34.19 16.53 8.83 65.72 48
where 0 ≤ MPC (k) ≤ 1. In general, an optimal cluster number k* is
Sand (%) 27.30 19.95 2.77 79.74 73 found by solving max2⩽k⩽n−1MPC(k) to produce a best clustering
Silt (%) 38.50 12.39 6.74 65.53 32 performance for the data set.
Hue 9.04YR 0.48YR 7.69YR 10.00YR 5
Value 3.14 0.74 1.64 5.15 23
Chroma 2.47 1.07 0.73 5.24 43 2.7. Predictive modeling and validation
X 8.22 4.08 2.37 22.58 50
Y 7.75 3.72 2.31 21.16 48 Predictive models for SOC, sand, silt and clay contents were cali-
Z 4.92 1.52 1.89 13.55 31 brated for each cluster and also for the MWS-260 and MWS-95. Data
x 0.38 0.02 0.34 0.43 6
were divided into two sets with 80% of samples for calibration (ran-
y 0.37 0.02 0.34 0.39 4
L 32.27 7.64 17.01 53.12 24 domly selected) and 20% for validation. Thus, the calibration sets of
a* 5.13 2.15 1.89 10.84 42 clusters 1, 2 and 3 contained 73, 76 and 59 samples, respectively (i.e.
b* 14.63 6.78 3.99 31.23 46 80% of the samples of each cluster). The validation sets of clusters 1, 2
u* 14.08 7.05 3.41 33.04 50
and 3 contained 18, 19 and 15 samples, respectively (i.e. 20% of the
v* 16.02 7.98 3.55 35.78 50
c* 15.52 7.10 4.41 32.82 46
cluster). In total, 208 samples were used to calibrate the models and in
h* 70.19 2.01 64.57 74.82 3 total 52 samples were predicted. To build the MWS-260 model, the
R 92.02 23.21 50.00 157.00 25 same 208 samples from the clusters were used to calibrate the model
G 73.78 15.29 44.00 120.00 21 and 52 samples were used for validation. MWS with 95 selected sam-
B 55.64 6.71 37.00 89.00 12
ples were also built, with a number of samples in the same range as the
C 19.03 0.16 19.00 20.00 1
M 26.65 3.23 22.00 35.00 12 clusters. Thus, the stratified and non-stratified groups are fully
Ye 33.76 6.94 23.00 52.00 21 equivalent and allowed a fair comparison of accuracy indices. Two
K 43.20 9.11 18.00 60.00 21 accuracy indices were used to assess the performance of the predictive
models: the coefficient of determination (R2v), which ranges from 0 to 1
SD: standard deviation; CV: Coefficient of variation.
and provides the percentage of variation explained by the model, and
the root mean square error (RMSEv), which measures the overall ac-
PC2 = (B1 .e2,1) + (B2 .e2,2) + ...+(Bn .e2,n)
curacy of the prediction model.
… In the prediction models, each time the model is run, a different R2
and RMSE value can be obtained, since random sampling is performed
PCn = (B1 .e n,1) + (B2 .e n,2) + ...+(Bn .en,n) (1)
in the sample set (randomized). To verify the variation in the prediction
where: PC is the principal component (scores); B is the original data of the models, the following simulations were performed: 1st) For each

6
J.J.F. Costa, et al.
cluster the prediction models were run 18 times (3 clusters × 18 re-
petitions = 54 prediction models for each soil property); 2nd) the same
was done for the MWS-260 and MWS-95. (1 group × 18 repetitions for
each soil property). The repetitions were defined according to the
power of the statistical test (95%) to verify the variability of prediction
of the models. Power is the probability that the null hypothesis will be
rejected in favor of the alternative hypothesis (Uttley, 2019). The power
of statistical testing was performed with the use of the stats R package
(R Development Core Team, 2017).
Thus, estimates were obtained considering the average of R2 and
RMSE, and the variation presented by the models. The models were
calibrated with the combination of the Vis-NIR-SWIR spectral curves
corresponding to each soil. Two multivariate methods were im-
plemented to evaluate the predictive performance: partial least squares
regression (PLSR) in the pls package (Liland, 2013) and support vector
machines (SVM) in the e1071 package (Dimitriadou et al., 2015). For
the comparison of the performance of the models, Student's t-test was
applied to RMSE values to check for differences between the means of
the clusters and of the MWS-260 and MWS-95. Student's t-test was
performed using the stats R package (R Development Core Team, 2017).
3. Results and discussion
3.1. Descriptive statistics
Soil organic carbon and sand have coefficients of variation (CV)
greater than 50%, characterizing the heterogeneity of these soil phy-
sical and chemical properties (Table 3). Silt was the soil property with
the lowest CV, followed by clay, 32 and 48%, respectively. The varia-
bility of SOC and sand contents is associated with the humic char-
acteristics of the soils conferred by climate condition, slope and geo-
logical formation of the area (Dalmolin et al., 2017). The presence of
altitude fields with accumulation of SOC in the superficial layers of the
soil, in the flat areas (shallow soils) and the formation of pine forests in
the slopes (deeper soils) are also responsible for the granulometric and
SOC content variability of the samples. This variability is reflected in
both the distribution of soil properties and quantified soil color mea-
surements (Table 3). Soil hues ranged from 7.69YR to 10.00YR, with
the value ranging from 1.64 to 5.15 units and chroma from 0.73 to 5.24
units. Since Munsell's soil color measurement is subjective (Post et al.,
1994), a Vis-based-color may provide fast quantitative measurements of
soil color (Viscarra Rossel et al., 2003) and assist in the selection of the
predominant soil color.
3.2. Principal component analysis (PCA)
According to the results of PCA (Fig. 3) in the first principal com-
ponent (PC1), which accounts for 84% of the total variation, virtually
all parameters had significant contribution values (0.92 on average)
except for h* (0.54) and C (0.41) which had the lowest positive con-
tribution values. The second principal component (PC2), accounting for
7%, is associated with a strong influence of Hue (0.86) and h* (0.83).
The color parameters that best determined the behavior of the soil
sample set were value, chroma, CIE Lb*, CIE Lv*c*, RG and MYK (0.92
on average) in the first axis and Hue (0.86) in the second axis. These
results are consistent with Viscarra Rossel et al. (2003) who, in their
studies of the most appropriate color models for quantitative descrip-
tion of soil color and its relationship with SOC contents, found that the
parameters lightness (L), R from RGB model and v* from CIE Lu*v*
model had higher correlations with SOC content. Similarly, Baumann
et al. (2016), when using soil color and spectroscopy to predict SOC,
found that lightness (L) has a good correlation with SOC contents.
Lightness parameters (L) vary according to geographic region and land
use and are related to SOC content (Spielvogel et al., 2004). The a*
value of CIE La*b* models is related to the red color of soils that may be
influenced by Fe oxides, mainly hematite. The b* value of CIE La*b*
7
Computers and Electronics in Agriculture 177 (2020) 105710
models is related to the yellow color of soils, reflecting differences in
geological and pedogenetic conditions (Fischer et al., 2010) and can be
an estimate of goethite content, with a good contribution (0.98) in PC1
(Fig. 3). Thus, Vis-based-color parameters can be applied to determine
soil color, mineral composition and clay content (Aitkenhead et al.,
2013a; Dominguez et al., 2010; Viscarra Rossel et al., 2009), and in the
identification of SOC content (Vodyanitskii and Savichev, 2017).
3.3. Cluster analysis
Fuzzy k-means (FKM) clustering was used to partition the soil
sample set into more homogeneous groups (clusters). Based on cluster
evaluations (Table 4) and considering the color parameter values, soil
samples were divided into 3 clusters. The first two PCA scores were
used, which explained 91% of data variability (Table 4). The choice of
the optimal number of clusters considered higher PC (0.99) and MPC
(0.99) values, indicating good partition and also lower PE values (0.02),
which imply a sharper partition (“crisp class”), as suggested by Bezdek
et al. (1984) and Viscarra Rossel et al. (2016).
In FKM grouping, soil samples were sorted according to their
characteristics. The average spectra of all samples in each cluster
showed similar spectral absorption peak characteristics (Fig. 5a).
However, there was a statistically significant difference in the mean
reflectance value of the clusters, particularly because of the difference
in mean SOC contents and the tendency for reflectance to decrease with
increased SOC contents. For example, cluster 1 had the highest mean
reflectance values and lowest SOC contents (4% on average) (Figs. 4a
and 5a). In contrast, cluster 2 had the lowest mean reflectance and the
highest SOC contents (18% on average). These findings are consistent
with (Liu et al., 2019), who applied cluster analysis to soil samples and
found that changes in SOC content affected soil clustering. A similar
spectral behavior was reported by Stenberg et al. (2010) and Nocita
et al. (2014) who found differences in reflectance for organic soils in the
NIR wavelength range. Another key aspect in spectral analysis is the
fact that the soils in cluster 2 had the highest contents of SOC and sand
(Fig. 4a and c). However, SOC has low reflectance and when it contains
materials with higher reflectance (such as quartz, the dominant com-
ponent of sand), it masks spectral response, reducing reflectance and
hence the contrast of material absorption features (Demattê et al.,
2019). Absorption at 2207 nm related to clay minerals was less evident
for cluster 2, as it grouped samples with lower clay content. By contrast,
absorption was more noticeable in cluster 1 because it grouped samples
with higher clay content (Fig. 4b and 5a).
Cluster 1 samples showed well-defined iron oxide (FeIII) absorption
features in the bands at 480, 550 and 850 nm (Fig. 5b), indicating the
presence of goethite and hematite (Dalmolin et al., 2005; Moura-Bueno
et al., 2019). Absorption bands were identified at wavelengths 1400
and 2200 nm due to molecular vibrations of OH and Al-OH groups in
clay minerals, mainly related to the presence of kaolinite and/or
montmorillonite (Dalmolin et al., 2005). In cluster 1, at certain wave-
lengths, higher energy absorption rates were observed because the
samples had clay texture and higher iron oxide content (FeIII), while in
the samples of clusters 2 and 3, with a lower percentage of clay and
lower oxide content, this behavior was not observed (Fig. 5a and b).
Soil organic carbon content influenced the shape and albedo of the
whole spectral curve (Fig. 5a and b). In the literature, this soil property
can have a greater influence in the region between 400 and 1000 nm.
This characteristic was observed in samples with high SOC content,
which showed reduced albedo throughout the spectral curve, mainly in
samples of clusters 2 and 3, but reductions were higher in the regions
between 400 and 1000 nm. This reduction in albedo due to a higher
SOC content was observed by Liu et al. (2019) and Moura-Bueno et al.
(2019) who found that SOC content variability influenced the behavior
of spectral curves.
J.J.F. Costa, et al. Computers and Electronics in Agriculture 177 (2020) 105710

Fig. 3. Result of principal component analysis of color parameters that best explained variation in soil informations based on soil color.

Table 4 respectively. In the SVM method, the cluster 3 obtained the best indices
Fuzzy k-means clustering assessments and selection of the optimal number of with mean values of R2 and RMSE of 0.82 and 2.7%, respectively. While
clusters considering the higher PC and MPC values and also lower PE values. cluster 2 obtained the highest mean values of RMSE of 2.9%. In the
Number Cumulative Indexes Number of Clusters prediction of clay content with the use of the PLSR method, the cluster
of Scores Variation% 2 obtained the best indices with mean values of R2 and RMSE of 0.72
8 7 6 5 4 3 2 and 7%, respectively. While cluster 3 obtained the highest mean value
RMSE of 9%. In the SVM method, the cluster 2 obtained mean values of
2 91 PC 0.93 0.95 0.95 0.98 0.97 0.99 0.98
PE 0.13 0.09 0.10 0.04 0.05 0.02 0.04 R2 and RMSE of 0.59 and 8.3%, respectively. While cluster 1 obtained
MPC 0.92 0.94 0.93 0.97 0.97 0.99 0.95 the lowest performance with mean values of R2 and RMSE of 0.30 and
3 96 PC 0.97 0.98 0.98 0.96 0.95 0.92 0.94
9.6%, respectively. When using the MWS with lower number of samples
PE 0.97 0.05 0.06 0.09 0.10 0.15 0.10 (n = 95), it was observed that the calibration models showed, on
MPC 0.97 0.98 0.97 0.95 0.94 0.88 0.89 average, a poor quality of prediction of the SOC content and clay
4 99 PC 0.97 0.99 0.99 0.96 0.93 0.90 0.92 fraction for the different multivariate models. For the SOC content the
PE 0.06 0.03 0.04 0.08 0.14 0.18 0.14 RMSE increased, on average, from 2.6 to 3.2% and from 2.6 to 3.3%,
MPC 0.97 0.99 0.98 0.96 0.91 0.86 0.84 using the SVM and PLSR models, respectively. Likewise, for the clay
fraction the RMSE increased, on average, from 8.8 to 10.7% and from
PC: partition coefficient; PE: partition entropy; MPC: modified partition coef-
8.8 to 11%, using the SVM and PLSR models, respectively. The results
ficient.
of the standard deviation indicate that there was greater absolute
variability of cluster validations (Table 5), especially for the cluster
3.4. Prediction performance of spectral models
containing soil samples with lower SOC contents. With the repetitions,
more accurate prediction values can be obtained, considering the
Assessment of the performance of the models considered the 18
changes in each model, without depending on the choice of the best or
repetitions for each prediction model (MWS-260, MWS-95 and clus-
worst prediction model.
ters). Thus, the average R2v and RMSEv values were considered to assess
In general, the error of the PLSR model (clusters and MWS-260) was
the performance of the two methods. The results (presented in Table 5)
smaller than those observed for the SVM model (Table 5). The mean
show changes in the prediction of soil properties, and the prediction
error of the models was often related to increased SOC content (Table 5
performances of the PLSR models, were on average better than those of
and Fig. 4a). For example, for cluster 1, the mean SOC content was 4%
SVM models. In SOC modeling, with the use of the PLSR method, the
and RMSE values were on average 1.2 and 1.4% for the SVM and PLSR
cluster 3 obtained the best accuracy rates, with mean values of R2 and
models, respectively. In turn, the mean SOC content of cluster 2 was
RMSE of 0.88 and 2.3%, respectively. While cluster 1 obtained the
18% and RMSE values were on average 2.9 and 2.6% for the SVM and
lowest indices with mean values of R2 and RMSE of 0.63 and 1.4%,

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J.J.F. Costa, et al. Computers and Electronics in Agriculture 177 (2020) 105710

Fig. 4. Statistical distribution and variability of SOC (a), clay (b), sand (c) and silt (d) contents for the model without stratification (MWS-260 and MWS-95) and
clusters. Median values, 1st and 3nd quartile.

PLSR models, respectively. According to Nocita et al. (2014) prediction with RMSE values of 8.3 and 7%, on average, for the SVM and PLSR
errors tend to increase with increase in SOC content. This result was models, respectively. In cluster 1, which had the highest clay content
confirmed by the low reflectance of cluster 2 (Fig. 5a), and is explained (45%, on average), RMSE values were 9.6 and 7.3% for the SVM and
by the higher OM content, which has low reflectance level and masks PLSR models, respectively.
the reflectance of the samples (Nocita et al., 2014; Stenberg et al.,
2010).
The mean error of the models increased with increase in clay con-
tent (Table 5). Cluster 2 had the lowest clay content (21% on average),

Fig. 5. Mean reflectance spectra of clusters based on color (a) parameters and the first derivative of spectral curves, highlighting spectral bands related to soil
components and changes in reflectance intensity (b).

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J.J.F. Costa, et al. Computers and Electronics in Agriculture 177 (2020) 105710

Table 5
Predictive performance of soil properties for the validation set considering the model without stratification (MWS-260 and MWS-95) and the performance of the
models after cluster analysis based on color parameters.
Cluster 1 (n − 91) Cluster 2 (n − 95) Cluster 3 (n − 74) MWS (n − 260) MWS (n − 95)

SVM PLSR SVM PLSR SVM PLSR SVM PLSR SVM PLSR

R2 RMSE R2 RMSE R2 RMSE R2 RMSE R2 RMSE R2 RMSE R2 RMSE R2 RMSE R2 RMSE R2 RMSE

SOC/Repet. % % % % % % % % % %
1 0.91 0.8 0.86 1.5 0.86 2.9 0.85 2.3 0.82 3.3 0.86 2.5 0.93 2.2 0.91 2.4 0.81 3.8 0.81 3.8
2 0.82 0.7 0.72 1.1 0.80 2.6 0.87 2.7 0.85 3.1 0.87 3.0 0.91 2.5 0.92 2.3 0.81 3.0 0.80 3.1
3 0.66 0.8 0.64 1.0 0.78 2.3 0.82 2.2 0.73 4.9 0.82 3.9 0.89 3.2 0.91 2.7 0.84 3.2 0.83 3.4
4 0.76 1.2 0.74 1.3 0.69 2.5 0.76 2.3 0.82 1.8 0.87 1.4 0.91 2.1 0.90 2.3 0.82 4.7 0.83 4.4
5 0.81 0.9 0.82 1.0 0.70 2.9 0.73 2.6 0.82 1.6 0.86 1.7 0.87 2.5 0.86 2.7 0.80 3.7 0.81 3.7
6 0.72 1.3 0.74 1.2 0.84 3.1 0.86 2.5 0.91 1.8 0.97 1.3 0.88 2.3 0.88 2.3 0.79 3.4 0.78 3.2
7 0.79 0.8 0.58 1.4 0.70 3.5 0.78 3.1 0.72 3.5 0.85 2.3 0.91 2.5 0.92 2.3 0.94 2.4 0.92 2.7
8 0.11 3.6 0.26 3.3 0.86 2.6 0.88 2.6 0.82 4.4 0.90 3.4 0.85 3.6 0.88 3.3 0.82 2.8 0.82 3.1
9 0.94 0.9 0.90 1.1 0.74 3.2 0.75 3.1 0.82 1.9 0.88 1.6 0.83 2.9 0.83 3.0 0.86 3.1 0.84 3.4
10 0.66 1.1 0.56 1.5 0.59 4.1 0.70 3.0 0.83 2.6 0.89 2.1 0.89 2.3 0.88 2.6 0.90 2.8 0.90 2.7
11 0.66 1.0 0.66 1.5 0.73 3.5 0.86 2.2 0.94 0.9 0.91 1.7 0.90 2.3 0.90 2.4 0.74 3.7 0.71 3.9
12 0.68 1.0 0.56 1.2 0.81 2.8 0.82 2.9 0.87 1.4 0.87 1.6 0.91 2.3 0.91 2.3 0.89 2.9 0.87 3.3
13 0.83 0.7 0.71 0.9 0.80 2.5 0.89 2.0 0.66 3.5 0.84 3.3 0.92 2.3 0.92 2.4 0.91 2.5 0.91 2.5
14 0.12 3.6 0.27 3.2 0.85 2.1 0.85 2.3 0.87 2.1 0.94 2.3 0.86 2.7 0.86 2.7 0.80 3.4 0.81 3.7
15 0.60 1.0 0.56 1.1 0.75 2.7 0.83 2.5 0.89 4.1 0.90 3.5 0.86 3.1 0.90 2.7 0.87 3.7 0.90 3.1
16 0.67 0.9 0.44 1.1 0.78 2.7 0.88 2.0 0.70 3.2 0.81 2.7 0.90 2.3 0.87 2.7 0.95 2.2 0.95 2.3
17 0.69 1.0 0.54 1.2 0.76 3.4 0.82 2.8 0.81 2.0 0.82 1.9 0.87 2.7 0.86 2.8 0.89 2.7 0.89 2.7
18 0.83 0.6 0.73 0.9 0.70 2.9 0.74 2.9 0.96 2.4 0.96 1.5 0.88 2.9 0.88 2.8 0.87 4.3 0.90 3.9
Mean 0.68 1.2 0.63 1.4 0.76 2.9 0.82 2.6 0.82 2.7 0.88 2.3 0.89 2.6 0.89 2.6 0.85 3.2 0.85 3.3
SD 0.23 0.9 0.18 0.7 0.07 0.5 0.06 0.4 0.08 1.1 0.05 0.8 0.03 0.4 0.03 0.3 0.06 0.7 0.06 0.6
Max. 0.94 3.6 0.90 3.3 0.86 4.1 0.89 3.1 0.96 4.9 0.97 3.9 0.93 3.6 0.92 3.3 0.95 4.7 0.95 4.4
Min. 0.11 0.6 0.26 0.9 0.59 2.1 0.70 2.0 0.66 0.9 0.81 1.3 0.83 2.1 0.83 2.3 0.74 2.2 0.71 2.3

Clay
1 0.63 6.4 0.67 6.0 0.82 8.1 0.90 5.4 0.76 7.2 0.88 5.4 0.76 8.2 0.77 7.9 0.73 9.9 0.74 9.7
2 0.19 10.5 0.64 6.4 0.80 5.5 0.88 4.3 0.77 8.9 0.90 6.3 0.77 8.3 0.76 8.4 0.49 11.9 0.34 14.4
3 0.56 8.0 0.67 6.7 0.71 7.8 0.86 5.4 0.90 6.9 0.88 6.8 0.71 9.2 0.67 9.7 0.59 12.6 0.65 11.7
4 0.34 9.5 0.50 6.9 0.80 7.1 0.81 7.3 0.84 7.4 0.82 7.5 0.76 8.4 0.81 7.5 0.60 11.0 0.67 10.0
5 0.47 8.5 0.61 6.9 0.59 6.4 0.79 5.2 0.65 9.4 0.70 8.0 0.70 8.7 0.73 8.1 0.65 11.5 0.67 11.0
6 0.46 8.2 0.59 6.9 0.81 5.6 0.79 5.9 0.62 9.2 0.75 8.8 0.76 7.7 0.72 8.3 0.72 11.4 0.71 10.9
7 0.24 9.5 0.51 7.1 0.23 11.1 0.78 6.0 0.62 9.8 0.66 8.8 0.64 9.8 0.65 9.3 0.78 8.0 0.85 7.0
8 0.43 8.0 0.54 7.2 0.69 8.4 0.77 6.8 0.75 7.9 0.82 8.9 0.71 8.7 0.74 8.3 0.45 11.5 0.54 10.8
9 0.16 10.3 0.48 7.2 0.63 10.2 0.76 7.9 0.70 9.8 0.74 9.1 0.65 10.2 0.67 9.9 0.91 6.3 0.87 7.7
10 0.27 7.8 0.27 7.4 0.60 8.1 0.68 8.7 0.66 9.3 0.68 9.5 0.79 7.8 0.72 8.9 0.63 10.8 0.64 11.6
11 0.20 9.2 0.39 7.6 0.52 7.8 0.67 6.4 0.47 11.3 0.62 9.7 0.74 8.9 0.73 9.1 0.48 13.1 0.41 12.9
12 0.30 9.4 0.52 7.7 0.63 6.6 0.66 6.3 0.69 9.9 0.68 9.7 0.73 8.4 0.67 9.2 0.73 9.4 0.72 9.5
13 0.02 13.4 0.48 7.8 0.69 7.0 0.66 6.9 0.76 9.3 0.79 9.8 0.81 7.4 0.78 7.9 0.69 9.9 0.67 10.1
14 0.44 9.3 0.56 7.8 0.50 8.5 0.65 8.0 0.52 11.8 0.61 10.4 0.59 10.0 0.63 9.6 0.74 8.5 0.59 11.2
15 0.38 9.6 0.64 7.9 0.48 10.1 0.61 9.6 0.51 12.3 0.57 10.6 0.71 9.1 0.72 8.9 0.70 11.7 0.71 10.5
16 0.18 11.9 0.60 7.9 0.34 13.0 0.60 10.1 0.63 12.0 0.74 10.9 0.75 8.3 0.71 8.9 0.66 9.7 0.45 13.0
17 0.17 10.4 0.64 8.0 0.39 11.7 0.54 10.0 0.66 10.7 0.80 11.2 0.72 8.7 0.74 8.4 0.53 12.9 0.45 14.5
18 0.00 12.9 0.50 8.0 0.44 7.0 0.54 6.3 0.48 13.3 0.64 11.3 0.69 10.1 0.71 9.7 0.63 11.9 0.66 11.1
Mean 0.30 9.6 0.54 7.3 0.59 8.3 0.72 7.0 0.67 9.8 0.74 9.0 0.72 8.8 0.72 8.8 0.65 10.7 0.63 11.0
SD 0.17 1.8 0.10 0.6 0.17 2.1 0.11 1.7 0.12 1.8 0.10 1.7 0.05 0.8 0.05 0.7 0.12 1.8 0.14 2.0
Max. 0.63 13.4 0.67 8.0 0.82 13.0 0.90 10.1 0.90 13.3 0.90 11.3 0.81 10.2 0.81 9.9 0.91 13.1 0.87 14.5
Min. 0.00 6.4 0.27 6.0 0.23 5.5 0.54 4.3 0.47 6.9 0.57 5.4 0.59 7.4 0.63 7.5 0.45 6.3 0.34 7.0

MWS-260: model without stratification using 260 soil samples.

MWS-95: model without stratification using 95 selected samples.

3.5. Prediction of soil properties using clusters and the MWS-260 and
MWS-95
Cluster analysis based on soil color affected the prediction of SOC
contents (Table 6 and Fig. 6). In general, the error obtained in the
clusters was smaller than the error obtained in the MWS-260 and MWS-
95. The mean comparison test of RMSE values for both methods was
presented with alpha level 0.05. According to the results obtained, all
soil property studied had significant error reduction and prediction
performances of the PLSR models, on average, were better than those of
SVM model. In the SOC modeling using the PLSR method, the mean
RMSE values were 2.6 ± 0.3 for the MWS-260 and 2.1 ± 0.8 for the
clusters, representing a 19% reduction in the prediction error. Likewise,
when using the MWS with 95 selected samples, the reduction of the
error was 36% (Table 6 and Fig. 6). For the SVM method, the mean
RMSE values were 2.6 ± 0.4 for the MWS-260 and 2.3 ± 1.1 for the
clusters, though not significant. However, when using the MWS with 95
selected samples, the reduction of the error was significant of 28% in
the prediction. These values are close to those observed in a study on
SOC prediction conducted by Jaconi et al. (2017), who applied cluster
methods based on soil depth, land use, pH, and soil texture data to
develop individual spectral models for each subset. According to the
authors, the stratification of the dataset reduced by 22% the error of the
clustered models compared to the MWS. Similarly, Nocita et al. (2014),
when predicting SOC content, selected soil samples based on spectral
distance and spectral combination with sand (predictor variable). Ac-
cording to the authors, prediction errors were higher in soils with
higher SOC content.
In clay prediction using the PLSR method, the mean RMSE values
were 8.8 ± 0.7 for the MWS-260 and 7.8 ± 1.6 for the clusters, re-
presenting a significant 11% reduction in the prediction error. Likewise,
when using the MWS with 95 selected samples, the reduction of the

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J.J.F. Costa, et al. Computers and Electronics in Agriculture 177 (2020) 105710

Table 6
Statistically significant difference and reduction of prediction error in the results of prediction with PLSR and SVM methods for each soil property.
Attributes Method Process Mean of RMSE value (%)* Error reduction (%)* Mean of RMSE value (%)** Error reduction (%)**

SOC PLSR Clusters 2.1 ± 0.8 a 19 2.7 ± 0.6 a ns

MWS-260 2.6 ± 0.3 b 2.7 ± 0.2 a
Clusters 2.1 ± 0.8 a 36 – –
MWS-95 3.3 ± 0.6 b – –
SVM Clusters 2.3 ± 1.1 a ns 2.7 ± 0.6 a ns
MWS-260 2.6 ± 0.4 a 2.7 ± 0.4 a
Clusters 2.3 ± 1.1 a 28 – –
MWS-95 3.2 ± 0.7 b – –

Clay PLSR Clusters 7.8 ± 1.6 a 11 10.0 ± 2.5 a ns

MWS-260 8.8 ± 0.7 b 9.3 ± 1.1 a
Clusters 7.8 ± 1.6 a 29 – –
MWS-95 11.0 ± 2.0 b – –
SVM Clusters 9.2 ± 2.0 a ns 10.0 ± 2.4 a ns
MWS-260 8.8 ± 0.8 a 9.3 ± 1.2 a
Clusters 9.2 ± 2.0 a 14 – –
MWS-95 10.7 ± 1.8 b – –

Sand PLSR Clusters 9.1 ± 3.5 a 17 10.5 ± 2.5 a ns

MWS-260 10.9 ± 0.7 b 10.8 ± 1.0 a
Clusters 9.1 ± 3.5 a 25 – –
MWS-95 12.2 ± 1.9 b – –
SVM Clusters 11.1 ± 4.6 a ns 11.0 ± 2.5 a ns
MWS-260 11.4 ± 0.6 a 10.6 ± 1.0 a
Clusters 11.1 ± 4.6 a ns – –
MWS-95 12.8 ± 2.1 a – –

Silt PLSR Clusters 9.2 ± 1.6 a ns 10.4 ± 1.8 a ns

MWS-260 9.7 ± 0.8 a 9.7 ± 0.7 a
Clusters 9.2 ± 1.6 a 12 – –
MWS-95 10.4 ± 1.8 b – –
SVM Clusters 10.4 ± 2.0 a ns 11.0 ± 2.1 a 12
MWS-260 9.9 ± 1.0 a 9.8 ± 0.7 b
Clusters 10.4 ± 2.0 a ns – –
MWS-95 10.5 ± 1.9 a – –

MWS-260: model without stratification using 260 soil samples; MWS-95: model without stratification using 95 selected samples; *Considering only the Vis region to
group soil samples; **Considering the Vis-NIR-SWIR region to group the soil samples; Equal letters indicate no statistically significant difference and different letters
indicate a statistically significant difference between mean RMSE values for the clusters and the model without stratification (MWS-260), according to Student’s t-test
at p < 0.05. ns, not significant.

error was significant of 29% for the PLSR and 14% for the SVM (Table 6
and Fig. 6). Regarding the prediction of sand content using the PLSR
method, error reduction was also significant, with mean RMSE values of
10.9 ± 0.7 for the MWS-260 and 9.1 ± 3.5 for the clusters, re-
presenting an 17% reduction in the prediction error. Likewise, when
using the MWS with 95 selected samples, the reduction of the error was
25%. For silt prediction using the PLSR method, the reduction of the
error was significant of 12% in the prediction, when using the MWS
with 95 selected samples. With the SVM method, the average RMSE
values of the clusters were higher than those in the MWS-260, in-
dicating the poor performance of this methodology in silt prediction.
Since the soils assessed in this study contained comprehensive in-
formation on various soil properties (Table 3 and Fig. 4), multivariate
analysis grouped soil samples based on color parameters and grouped
the complex dataset into clusters with similar spectral characteristics,
thus reducing the possible interference of the variability of these
properties in prediction (Guerrero et al., 2010; Shi et al., 2015). In
contrast, the MWS-260 had soil samples with greater data variability,
resulting in a higher prediction error. Thus, data variability represented
by mean and standard deviation, influenced the final accuracy of the
prediction models, as expressed in R2 and RMSE. The results revealed
that the prediction using data with larger variability have higher R2,
but, in contrast, there was an increase in the mean values of the RMSE,
which is not desirable, since the higher the mean square error, the
greater the differences between the predictions and estimated value.
According to Guerrero et al. (2014) and Moura-Bueno et al. (2019) if
soil samples are similar to the overall prediction set, the model will
provide more accurate results.
When comparing the sample grouping methods (Table 6), the
method that considered only the Vis region obtained the largest dif-
ference between the mean RMSE values (for clusters and MWS-260),
with significant reductions in error for SOC content (19%, PLSR
method), clay (11%, PLSR method) and sand content (17%, PLSR
method). While the method that considered the Vis-NIR-SWIR did not
show significant reductions among the mean RMSE values.
Following the application of this methodology, it is necessary to
understand why color parameters grouped the samples based on the
relationships between soil features and color. For some soil properties
the explanation for a relationship with soil color may be clearer than for
other properties, for example: (a) organic matter is a primary con-
stituent of soil color, imparting dark colors to surface horizons and
some subsurface horizons (illuviation); b) quartz (in the sand) gives the
soil a white color, increasing the intensity of soil reflectance; and c) iron
oxides (FeIII) present in well-drained and weathered soils, impart
mainly a red (hematite) or yellow (goethite) color (Aitkenhead et al.,
2013a). Each of these factors impact soil color, thus allowing the es-
tablishment of clustering techniques based on color parameters.
Unlike other attempts to improve prediction models, the present
study sought simpler solutions, which do not entail additional costs, to
increase the potential to improve the prediction of soil properties. Other
approaches used simple stratification methods based on soil depth, pH
and texture to divide the data into subgroups (Jaconi et al., 2017). The
strategies for clustering soil samples are generally based on soil prop-
erties according to depths and also the types of land use and cover, or
their combinations (Stevens et al., 2013; Vasques et al., 2010). Stevens
et al. (2013) added new predictors to the spectral matrix in an attempt
to improve the models of prediction of SOC content. These authors
tested sand and clay fractions as auxiliary predictors. However, as with

11
J.J.F. Costa, et al.
Fig. 6. Performance of prediction models considering the model without stratification (MWS-260 and MWS-95) and performance of the models after cluster analysis
based on color parameters. Median values, 1st and 3nd quartile.
SOC, these soil physical properties also need to be determined in the
laboratory. Moreover, using them as predictor variables makes pre-
diction more expensive. In contrast, clustering samples by color does
not entail higher costs, as color can be obtained from color parameters
derived from spectral curves (Vis). Moreover, this is a promising
method that can be used in laboratories for more accurate results in the
determination of soil properties.
The potential for discrimination of multivariate statistical analysis
applied to color parameters was possible due to the variability of soil
characteristics for SOC content and texture. Thus, in the grouping of
samples it was possible to divide 3 clusters with well-defined patterns.
In a set of soils with greater variability in their features, the potential of
this methodology could be even greater.
4. Conclusions
This study used color parameters derived from the visible spectrum
to group soil samples in order to predict soil physical and chemical
properties. Moreover, we compared the different prediction models:
both the models of the sample sets grouped based on color parameters,
as well as the models without stratification using 260 soil samples and
95 selected samples (MWS-260 and MWS-95). Multivariate statistical
analysis applied to color parameters were able to group soil samples
with similar characteristics, reducing data amplitude and improving the
accuracy of predictions of soil properties.
There was a reduction in prediction error with stratification, which
was significant for soil organic carbon (SOC) content, followed by clay,
sand and silt content. Prediction errors for SOC content using the PLSR
model were on average 2.6 ± 0.3% for the MWS-260 and 2.1 ± 0.8%
for clusters, representing a 19% reduction in the prediction error.
However, when using the MWS with 95 selected samples, the error
reduction was greater, of 36% in the prediction.
For clay content, prediction errors using the PLSR model were on
average 8.8 ± 0.7% for the MWS-260 and 7.8 ± 1.6 for clusters,
representing an 11% reduction in prediction error. However, when
12
Computers and Electronics in Agriculture 177 (2020) 105710
using the MWS with 95 selected samples, the error reduction was
greater, of 29% for the PLSR and 14% for the SVM. Overall, the PLSR
model performed better than the SVM model, as confirmed by the
statistical difference between RMSE results.
Therefore, the use of Vis-based-color parameters to group soil
samples can be a quick and inexpensive way to increase the potential of
spectroscopy to accurately predict soil physical and chemical proper-
ties.
CRediT authorship contribution statement
José Janderson Ferreira Costa: Conceptualization, Methodology,
Software, Investigation, Data curation, Writing - original draft, Writing
- review & editing, Visualization. Élvio Giasson: Conceptualization,
Methodology, Writing - review & editing, Supervision. Elisângela
Benedet da Silva: Methodology, Software, Investigation, Writing - re-
view & editing. João Augusto Coblinski: Software, Writing - review &
editing. Tales Tiecher: Conceptualization, Methodology, Writing - re-
view & editing, Supervision.
Declaration of Competing Interest
The authors declare that they have no known competing financial
interests or personal relationships that could have appeared to influ-
ence the work reported in this paper.
Acknowledgments
The authors thank the Coordination for the Improvement of Higher
Education Personnel (CAPES) - Finance Code 001 for the PhD scho-
larship. The second author thanks the National Council for Scientific
and Technological Development (CNPq) for the research productivity
grant. To the Graduate Program in Remote Sensing of the UFRGS for the
use of the equipment for Vis-NIR-SWIR spectrum measurements. The
J.J.F. Costa, et al.
Biodiversity Research Program, Atlantic Forest, Santa Catarina (PPBio-
MA-SC) and Agricultural Research and Rural Extension Corporation of
Santa Catarina (EPAGRI) for providing the data.
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