Geoderma 355 (2019) 113908

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Geoderma
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Determining the features influencing the-S soil quality index in a semiarid T

region of Iran using a hybrid GA-ANN algorithm
⁎
Hosein Shekofteha, , Azam Masoudib
a
Department of Soil Sciences, Faculty of Agriculture, University of Jiroft, Jiroft 61167-78671, Jiroft, Iran
b
Department of Soil Sciences, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran

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

Handling Editor: Alex McBratney S index as a soil physical quality is the slope of the soil water release curve on a mass base at its inflection point
Keywords: on a logarithmic matric potential scale. It is necessary to select the most influential soil properties on S index to
Regression predict it. In the current study, to select properties that influence S index, a hybrid algorithm: genetic algorithm
Pedotransfer functions (GA) in combination with an artificial neural network (ANN) was designed. The potential power of the GA-ANN
Soil quality algorithm in setting up a framework for identifying the most determinant parameters of S index in an Iranian
Soil water characteristics curve semiarid region was also investigated. Results of GA-ANN algorithm for selecting best dataset showed that five
properties including soil organic matter (SOM), sand, clay, carbonate calcium equivalent (CCE), and bulk density
(BD) had the lowest error. The ANN method resulted in a higher model efficiency (R2 = 0.92, RMSE = 0.00065
and MAPE = 0.14% than MLR (multiple linear regression (approach (R2 = 0.0.016, RMSE = 2.72 and
MAPE = 43. 16%). Results of sensitivity analysis for the ANN model showed that BD and CCE had the highest
and the lowest effects on S index, respectively. Considering the sensitivity analysis results and also that fact that
measurement of the S index is not cost-efficient, it is suggested that bulk density be used as an indicator of soil
quality.

1. Introduction
The quality of a soil is defined as follows: its capacity to function
within land use and ecosystem boundaries, continue biological pro-
ductivity, preserve environmental quality, and further plant, animal,
and human health. Although soil quality cannot be directly measured, it
can be evaluated with the help of soil quality indicators. Recently, S
index has been well known as an important indicator of soil physical
quality, first proposed and discussed by Dexter (2004b). It is the slope
of the soil water release curve (SWRC) on a mass base at its inflection
point on a logarithmic matric potential scale. S index was applied an
“easy and unambiguous measure” (Dexter, 2004b) through observa-
tions on various soil properties; these observations were integrated for
obtaining of soil physical indicators (SPQIs). Several researches have
proved suitability of S index for identification of SPQIs. For instance,
according to Dexter (2004a, 2004b) S index correlates with several
important soil physical properties. As he stated, textural and structural
pores, in the SWRC, are represented as pores smaller and larger than
those corresponding with the inflection point, respectively. S index is
used as an indicator of SPQIs because soil physical degradation is al-
ways related to some change in the distribution of the structural pore,
leading to a change in the shape of the SWRC and in turn in the S value.
Dexter et al. (2007) insisted on two additional supporters of the S as an
adequate SPQI index: first, “the same S values have the same physical
meaning in widely different soils;” this is not true about “other soil
physical properties such as bulk density” (BD). Second, with the help of
the S, a more objective measurement with higher resolution (low
coefficient of variation and standard error) is provided, compared with
other measures, e.g. subjective visual examination of the SPQIs in the
field. The S was theoretically defined as a measure of soil micro-
structure, which would directly allow estimation of several important
soil physical properties by its value.
Though correlation of S index with other soil physical properties has
been studied, according to our knowledge, there is still a lack of enough
research about selection of appropriate soil properties for predicting S
index. This study tries to fill this gap and suggest further studies.
Feature selection (FS) is the best approach for selecting important
properties. FS is generally employed in machine learning. It is espe-
cially helpful when the learning task involves datasets with a lot of
dimensions. It is mainly aimed at choosing a set of features or properties
by throwing out those which have low predictive information as well as
the strongly correlated redundant properties (Vieira et al., 2010). The

⁎
Corresponding author.
E-mail address: h.shekofteh@vru.ac.ir (H. Shekofteh).

https://doi.org/10.1016/j.geoderma.2019.113908
Received 23 February 2019; Received in revised form 8 July 2019; Accepted 7 August 2019
Available online 17 August 2019
0016-7061/ © 2019 Elsevier B.V. All rights reserved.
H. Shekofteh and A. Masoudi
availability of an array of input data poses a challenge to the more
conventional statistical methods such as regression and classification
analysis. For instance, the employment of various input features for
deriving a pedo-transfer function to predict the S index may require
estimation of a sizable number of parameters in a regression analysis
hence more data points to be measured. In an ideal situation, for each
feature which is input in a regression analysis, a separate set of in-
formation should be added. If the input variables are strongly corre-
lated, the redundancy of the available information may impact the
accuracy of the regression model negatively (Pal and Foody, 2010).
Recently, meta-heuristic algorithms, inspired by the nature, have been
employed for feature selection purposes in soil science. See Shirani
et al. (2015) for an example of a particle swarm optimization (PSO) for
selecting the most influential properties on soil physical quality indices
and Shekofteh et al. (2017) for an application of ant colony organiza-
tion optimization (ACO) for selecting effective properties on soil CEC.
One of the nature inspired meta-heuristic algorithms is genetic al-
gorithm (GA). In this study, a hybrid algorithm GA-ANN (Artificial
Neural Network) was used for selecting the best subset affecting the S-
index.
The aims of this study were as follows: to assess the GA in combi-
nation with ANN to select the best set of input properties influencing
the S index, to do modeling after selecting the properties that influence
the S index by ANN and multiple llinear regression (MLR) approaches,
and to compare ANN and MLR results.
2. Materials and methods
2.1. Study area
The studied area of the present study was the same as the area
studied in Shekofteh et al. (2017). To select the set of features which
affect S index, soil samples from parts of Rabor Region (29° 27′ N to 38°
54′ N and 56° 45′ E to 57° 16′ E) were collected. Robor, a city in the
south east of Kerman province, is a semiarid farming area which has
cold temperature. The mean annual temperature of Rabor is 15 °C and
its annual precipitation is 250 mm. According to the Soil Survey Staff
(2014), the soils studied belonged mainly to Typic Calcixerepts sub-
group. The main textural classes in the area are loam and sandy loam.
2.2. Soil sampling and measurement
In the present study we used the soil samples and measurements
used in Shekofteh et al. (2017). In that study the authors collected 104
soil samples from the soil surface (0–15 cm depth) with four different
vegetation cover, including gardens with 20 year-old walnut trees,
pasture, agriculture, and a mountain almond forest. They took dis-
turbed and undisturbed samples to measure physical and chemical soil
properties. The disturbed soil samples were air-dried and ground to pass
a 2 mm sieve. Walkley-Black method with dichromate extraction and
titrimetric quantization (Nelson and Sommers, 1982) was used to de-
termine the content of soil organic carbon. Sieving and sedimentation
method (Gee and Bauder, 1986) was used to measure the percentages of
clay (> 0.002 mm), silt (0.002–0.05 mm) and sand (0.05–2 mm) par-
ticles. Blake and Hartge (1986) and the back-titration methods (Nelson,
1982) were used to determine particle density (PD) and carbonate
calcium equivalent (CCE), respectively. A digital pH meter (Thomas,
1996) and an electrical conductivity meter (Rhoades, 1996) were sued
to measure pH and determine electrical conductivity, respectively. Also
undisturbed soil samples were taken using 100 cm3 core samples to
determine the soil bulk density based on the core method (Klute, 1986)
and to obtain the soil water retention curve (SWRC).
To draw SWRC, soil water content was measured at 0, 15, 25, and
55 cm H2O suctions by hanging water column, and at 0.1, 0.2, 0.3, 0.5,
1, 2, 3, 5, and 10 bar pressure heads by pressure plate (Klute, 1986;
Klute, 1986). S index was determined in all soil samples by using the
2
Geoderma 355 (2019) 113908
moisture retention curve data. Soil texture, bulk density and moisture
retention curve data were used as input data in RETC 6.0 software and
the parameters of the equation (n and θr) (Van Genuchten, 1980) were
predicted. Then S index was calculated as follows (Dexter, 2004b):
1 −(1 + m)
S = −n (θsat − θr ) ⎡1 + ⎤
⎣ m⎦ (1)
If m = 1–1/n is applied:
1
2n − 1 ⎡⎣ n − 2⎤⎦
S = n (θsat − θr ) ⎡ ⎤
⎣ n−1⎦ (2)
−1
where n (empirical parameter), and θr (residual water content (gg ))
are obtained by RETC software but θsat (saturated water content
(gg−1)) was measured. Since S index is always negative, the modulus of
S index was used in this paper.
2.3. Selection of features affecting the S index
In this research nine properties were considered as follows: elec-
trical conductivity, sand, silt, clay, CCE, BD, PD, soil pH, and SOM as
the inputs and S index as the output.
Below is given a summary of GA and ANN method.
2.3.1. Genetic algorithm
GA works on the basis of the evolution theory in biology: the more
fitted a population, the more probable the continuation and reproduc-
tion of its subsequent. Main data set in GA consists of N features that are
first divide into the subsets d1, d2, d3 … with n1, n2, n3 members.
Afterwards, these subsets are transferred to the artificial neural network
(ANN). In the ANN, data are again divided into two parts: train and test,
with a ratio of 70 to 30, respectively. Data errors are then computed.
The error (root mean square error (RMSE)) is obtained by the sum of
the weights for train and test data errors as follows:
RMSE final = 0.7RMSEtrain + 0.3RMSEtest (3)
The mean error for 50 runs of the ANN model is considered as the
final error for each result. Next, the GA computes data fitness with
regard to error value; the best subset is selected based on its value.
2.3.2. ANN
This study made use of ANN to reach two goals: 1. The ANN as error
evaluator of the GA for choosing the most influential features, 2.
Prediction of the S index and comparison of the results from this pre-
diction with the multiple linear regression.
The most applicable ANN is the multi layer perceptron (MLP). The
general model for MLP is the feedforward networks with the Back
Propagation train algorithm. The latter networks are those in which the
first layer neurons are connected to the next layers; this connection
process is repeated in each layer to finally reach the output layer. Back
Propagation means that after the identification of the network output,
the weights of the last layer and the weights of the previous layers are
corrected, respectively. The MLP networks are composed of three main
layers: one input layer, one hidden layer and one output layer.
2.3.3. The GA-ANN for feature selection
Below are the details of how the combined algorithm is im-
plemented:
In the proposed hybrid GA-ANN model, different combination were
first randomly produced by GA according to the number of input fea-
tures where each combination was a chromosome. The first feature was
selected from each combination. Next, the error was computed using
the ANN model. Therefore, the fitness value of each chromosome was
determined by RMSEfinal. A three-layered feed-forward ANN was em-
ployed to evaluate combination. Table 1 shows the summary of the
parameters used in hybrid GA-NN model.
H. Shekofteh and A. Masoudi Geoderma 355 (2019) 113908

Table 1 Every value of the independent variable x is associated with a value of

Parameters of hybrid GA-ANN model. the dependent variable Y. The population regression line for n input
Parameter Setting variables x1, x2, …,xn is as Y = β0 + β1x1 + … + βn. Where Y de-
notes the dependent variable, β0 is a constant called the intercept,
Population size 50 x = (x1, …,xn) is a vector of input variables and β is the vector of re-
Crossover rate 0.75
gression coefficients (one for each explanatory variable). The observed
Cost function The root mean square error
ANN learning algorithm Levenberg-Marquardt
values for Y vary in their means and are assumed to have the same
ANN activation function Tangent-sigmoid standard deviation ε. In this study, SPSS software (IBM Inc., USA) was
Selection method Roulette wheel used to develop the MLR model.
Generation numbers 100
Chromosome size 9
Mutation rate 0.06
2.5. Evaluation criteria

The capability of the proposed models to predict the S index was

Table 2 checked using mean absolute percentage error (MAPE), the root mean
Statistics of physicochemical properties of soils under studied area. square error (RMSE), and coefficient of determination (R2) between
measured and predicted values. The MAPE, RMSE and R2 are denoted
Maximum Minimum Mean CV (%)
as below:
EC (dS m−1) 2.21 0.325 0.69 44.94 n
pH 7.99 6.74 7.75 2.78 ⎛1 Y (pi) − Y (oi) ⎞
Clay (%) 23.5 5.5 12.61 31.5
MAPE = ⎜
n
∑ Y (oi) ⎟ × 100
Silt (%) 43.5 9.5 31.47 15.81 ⎝ i=1 ⎠ (4)
Sand (%) 85 36.5 55.91 13.54
n
SOM (%) 7.93 0.23 2.2 82.39 1
Porosity 0.57 0.32 0.46 10.77
RMSE =
n
∑ [Y (pi) − Y (oi)]2
BD (g cm−3) 1.66 0.96 1.27 10.48
i=1 (5)
PD (g cm−3) 2.74 1.98 2.37 5.77 2
CCE (%) 47.28 0.99 12.1 62.77 n
⎧ ∑i = 1 (Y (pi ) − Yp)(Y (oi ) − Yo) ⎫
R2 =
⎨ ∑n (Y (p ) − Yp)2 (Y (oi ) − Yo)2 ⎬
EC: electrical conductivity, BD: bulk density, PD: particle density, CCE: carbo- ⎩ i=1 i ⎭ (6)
nate calcium equivalent; SOM: soil organic matter, CV: coefficient of variation.
here Y(pi) and Y(oi) are the measured and predicted SPQIs values re-
0.00375
spectively; Yp and Yo are the means of measured and predicted SPQIs
values and n is the total number of observations.
0.0037

0.00365 3. Results and discussion

RMSE (%)

0.0036 3.1. Statistical analysis of data

0.00355
0.0035
0.00345
0.0034
0 2 4 6 8 10
Number of featureas
Fig. 1. Obtained RMSE (%) values in selecting feature numbers using GA-ANN
hybrid algorithm for the prediction of S index.
In the next step, a selection approach was employed for selecting the
two fittest chromosomes for reproduction. A single point crossover
operator was employed for introducing new chromosomes to the next
generation and a mutation operator (a reversed mutation) was used for
creating new information in the offspring (Table 1). Subsequently, the
previous population was replaced by the new one and the steps above
were repeated until the generation number reached its maximum. In
this way, the best feature subset with one feature was identified. This
procedure was continued until the combination including 9 features
was evaluated. Finally, the subsets with 1to 9 features were compared
and the subset which had the lowest error was considered as the best
subset.
2.4. Multiple linear regression (MLR)
Linear regression is the oldest statistical technique in regression and
it could be considered as a benchmark approach for new techniques.
MLR technique which is the same as other regression techniques at-
tempts to model the relationship between two or more input variables
and a response variable by fitting a linear equation to observed data.
Table 2 displays descriptive statistics for the physical and chemical
properties of soil which have been used to select the set of features that
affect S index best. The content of SOM ranged between 0.23 and 7.93%
with a mean of 2.2%. Clay content varied between 5.5 and 23.5% with
a mean of 12.61%. Generally speaking, USDA soil texture in the studied
area was classified as sandy loam. The content of CCE ranged between
19.9 and 47.2% with a mean of 19.1%. Thus it can be concluded that
under an arid climate, the soil studied is calcareous. Soil pH varied
between 6.7 and 7.9 with a mean of 7.7. Soil pH had the lowest var-
iation among all the measured variables. The small variation of soil pH
can be contributed to the buffering capacity due to the high content of
calcium carbonate. Soil bulk densities varied between 1.6, 0.96 with a
mean of 1.2 g cm−3 and the soil particle densities ranged between 2.7
and 1.9 with a mean of 2.3 g cm−3. Soil EC varied between 0.325 and
2.2 dS m−1.
3.2. Selection of features affecting S index using the GA-ANN
Based on the GA-ANN analysis, a combination of five features in-
cluding SOM, CCE, clay, sand, and BD was introduced as the more
important combination of easily available soil properties which affected
the S index with a RMSE value of 0.00345% (Fig. 1). Adequate amounts
of SOM have a significant role in creation of good structure. In fact,
SOM improves aggregate stability and structural formation. It also in-
crements porosity, aids in water and air infiltration, promotes water
retention, and pore stability. Thus, SOM influences the shape of soil
retention curve and the S index. In a similar research by Shirani et al.
(2015) organic matter was a significant soil property that influenced
soil physical quality indices. S index and clay contents are related due
to the impact of the latter on soil porosity and structure formation. This

3
H. Shekofteh and A. Masoudi Geoderma 355 (2019) 113908

Train data
0.036 y = 0.913x + 0.0031
R² = 0.9519
0.0358

0.0356

Predicted S index
0.0354

0.0352

0.035

0.0348

0.0346
0.0348 0.035 0.0352 0.0354 0.0356 0.0358 0.036 0.0362
Observed S index

0.0358
Test data y = 0.9313x + 0.0024
0.0357
R² = 0.9251
0.0356
0.0355
Predicted S index

0.0354
0.0353
0.0352
0.0351
0.035
0.0349
0.0348
0.0348 0.035 0.0352 0.0354 0.0356 0.0358
Observed S index

Fig. 2. Comparison of the predicted and measured S index of the ANN model.

is because adequate amounts of clay particles in soils have a con-
siderable role in creation of a good structure. In addition, clay particles
have high water retention capacity owing to their particularly high
surface area. Also, having strong adhesion and plasticity, they provide
good soil structure. This way, they affect the moisture curve shape and
S index, itself obtained by the former.
The BD as a soil structural property has an influence on soil-invol-
ving processes including water flow, solute transport and air flow. The
BD shows the compact status of soil and the volume of soil pores in-
directly. Changes in soil BD affect such a variety of properties and
processes as porosity, pore size distribution, water retention capacity,
and air capacity. As such, S index, itself a soil structural index, is subject
to change too. In an assessment of influential factors on soil physical
destruction by Dexter et al. (2007) S index decreased with an increase
in bulk density.
Sand particles were one of the most influential features on the S
index. The soils under study had a high sand percentage. Despite having
a low specific surface area, low surface charge and inability in adhering
soil particles and soil structure, sand particles have a significant impact
on water flow in soil and shape of retention curve owing to their macro
pores. Therefore, they influence S index, which is obtained by moisture
curve.
The other influential feature on S index was CCE. With respect to
high percentage of CCE in the studied area (due to its existence in the
semi-arid location and non-leaching), this cementing factor causes soil
particles flocculation, aggregate formation and improvement of the soil
structure. Regarding CCE impact on soil structure, carbonates act as a
source of Ca+2 and help flocculation of clay particles.
The pH, EC, PD and silt properties were considered redundant fea-
tures among the input parameters. Thus, they were not used in the
databases for modeling S index. Electrical conductivity is indicative of
soluble salts concentration, which causes flocculation of clay particles
by reducing thickness of the diffuse double layer. Since the values
measured for the electrical conductivity (EC) of the studied soil samples
were low and had a limited range, they were not likely sufficient (see
Table 2) to result in significant differences on the S index. Conse-
quently, the GA-ANN algorithm did not recognize it as a discriminating
property. Likewise, the pH variable was removed from the input
parameters due to its limited variation in the study area (Table 2). In
fact, as an explanatory property, pH contributes to chemical inter-
pretation of soil. Nevertheless, for having a substantial influence on the
soil structure, it needs to be in a wide range. Another redundant feature
was silt content due to its close relationship and correlation with other
soil texture components. Soil particle density is another redundant
feature that can be calculated by SOM and soil mineral matters. One
reason behind feature selection is to remove redundant and correlated
parameters. Since soil particle density was correlated with SOM and soil
mineral matter, it was regarded as a redundant.

4
H. Shekofteh and A. Masoudi Geoderma 355 (2019) 113908

Train data
0.0365
0.036
0.0355
0.035

Predicted S index
y = 0.7897x + 0.0066
0.0345 R² = 0.0404
0.034
0.0335
0.033
0.0325
0.032
0.0315
0.033 0.0335 0.034 0.0345 0.035 0.0355 0.036 0.0365
Observed S index

Test data
0.036
0.0355
Predicted S index

0.035
0.0345
0.034
0.0335
0.033 y = 1.904x - 0.0326
R² = 0.0165
0.0325
0.032
0.0315
0.0349 0.03495 0.035 0.03505 0.0351 0.03515 0.0352
Observed S index

Fig. 3. Comparison of the predicted and measured S index of the MLR model.

18

16

14

12
Sensitivity index

10

0
Sand Organic matter Bulk density Clay CCE

Fig. 4. The sensitivities of RMSE derived by ANN model to removals of soil physicochemical properties.

5
H. Shekofteh and A. Masoudi
3.3. Modeling of S index after selecting proper features
As already mentioned, in this section the dataset was randomly
divided into two sets: training data set (70%) and testing data set
(30%). The MAPE and RMSE values between the proposed ANN model
and the observed S index for the training data were 0.11% and 0.0046,
respectively. The obtained coefficient of determination (R2) value be-
tween the observed and predicted S index using ANN values for the
training data was 0.95 (Fig. 2). The MAPE and RMSE values between
the proposed ANN model and observed value for the testing data were
0.0065 and 0. 14%, respectively. The coefficient of determination (R2)
obtained for the observed and predicted S index using the proposed
ANN values for the testing data was also 0.92 (Fig. 2).
The MAPE and RMSE values for the MLR model and the observed S
index for the training data were 39.54 and 2.05, respectively. The R2 for
the MLR and observed S-index for the training data was 0.04 (Fig. 3).
Moreover, the MAPE and RMSE values between MLR model and the
observed S index for the testing data were 43.16 and 2.72, respectively.
The obtained coefficient of determination (R2) between the measured
and predicted S index for the testing data using the proposed MLR
model was also 0.0016 (Fig. 3).
The results for the training data show that ANN model could capture
the relationship between the input parameters and the S index with
more accuracy than the MLR model. The values of performance criteria
for the testing data show that ANN is a more accurate approach than
MRL in predicting the S index in the studied area.
Based on the evaluation indices, it appears that conventional re-
gression model is very poor in predicting S index. These results suggest
that conventional regression techniques (i.e. multiple linear regression)
may not be reliable for predicting S index in the studied site.
Actually, multiple linear regression is only able to identify linear
relationships between dependent and independent variables. In case
there is a non-linear relationship between these variables, efficiency of
these models will decrease significantly.
So far, wide research has showed superiority of ANN over MLR
(Ingleby and Crowe, 2001; Amini et al., 2005; Asadi and Bagheri,
2010).
3.4. Sensitivity analysis of the ANN model
Given that only the ANN's accuracy was acceptable in predicting the
S index, the sensitivity analysis was done by the ANN. Results of RMSE
sensitivities for ANN are shown in Fig. 4. The figure indicates that BD,
sand, SOM, clay and CCE have the highest effect on the S index, in the
order of appearance.
Further to the sensitivity analysis, the S index had the highest sen-
sitivity to bulk density (BD), indicating that BD is the most important
structural index. Regarding that BD is more easily measurable than the
S index, it can be used as a substitute for the latter. More research can
be done on BD optimization limits.
After BD, the sand particles had the highest effect on the S index.
With regard to the high percentage of sand in the soil of the studied
area, the obtained results seem reasonable. However, as to the S index,
it can be said that it is not just an index of soil structure because soil
Geoderma 355 (2019) 113908
water characteristic curve can be affected by both soil texture and
structure. About Dexter (2004a) stated that the effect of organic matter
on soil S index is greater when clay content is low. In the study areas,
clay content was low; thus, organic matter had a more effect on the S
index.
4. Conclusion
The results of this study indicate that the GA-ANN has the ability to
provide an appropriate framework for selection of the most influential
features on S index. The GA-ANN can be applied to similar areas and
issues. According to the results, the neural network has better accuracy
in predicting the S index than the linear regression. Its accuracy is ac-
ceptable regarding prediction of the S-index.
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