Journal Pre-proof Spatial prediction of soil organic carbon using machine learning techniques in western Iran
Hamid Mahmoudzadeh, Hamid Reza Matinfar, Ruhollah Taghizadeh-Mehrjardi, Ruth Kerry PII:
S2352-0094(20)30009-2
DOI:
https://doi.org/10.1016/j.geodrs.2020.e00260
Reference:
GEODRS 260
To appear in:
Geoderma Regional
Received date:
2 July 2019
Revised date:
6 February 2020
Accepted date:
7 February 2020
Please cite this article as: H. Mahmoudzadeh, H.R. Matinfar, R. Taghizadeh-Mehrjardi, et al., Spatial prediction of soil organic carbon using machine learning techniques in western Iran, Geoderma Regional(2020), https://doi.org/10.1016/j.geodrs.2020.e00260
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© 2020 Published by Elsevier.
Journal Pre-proof
Spatial prediction of soil organic carbon using machine learning techniques in western Iran Hamid Mahmoudzadeh a, Hamid Reza Matinfar a, Ruhollah Taghizadeh-Mehrjardi
b,c
,
Ruth Kerryd a
Department of Soil Science, College of Agriculture, Lorestan University, Khorramabad,
Department of Geosciences, Soil Science and Geomorphology, University of Tübingen,
ro
b
of
Iran (
[email protected])
Tübingen, Germany (ruhollah.taghizadeh-
[email protected])
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Faculty of Agriculture and Natural Resources, Ardakan University, Ardakan, Iran
(
[email protected]) Department
of
Geography,
Brigham
Young
University,
Provo,
UT,
USA
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d
re
c
ur
na
(
[email protected])
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Corresponding author: Hamid Reza Matinfar
Department of Soil Science College of Agriculture Lorestan University Khorramabad, Iran
Email:
[email protected]
Spatial prediction of soil organic carbon using machine learning techniques in western Iran
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Abstract Estimation of soil organic carbon (SOC) is very useful for accurate monitoring of carbon sequestration. However, there are still significant gaps in the knowledge of SOC reserves in many parts of the world, including western Iran. To partially fill the gap, 865 soil samples were used with 101 auxiliary variables and 5 machine learning (ML) algorithms
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to digitally map SOC for the plough layer (0-30 cm) at a 90-m resolution in Kurdistan
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province. Results indicated that the most important auxiliary variables were rainfall
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(27.09 %), valley depth (26.66 %), terrain surface texture (23.42 %), air temperature
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(20.18 %), channel network base level (16.61 %) and terrain vector roughness (14.47 %). Results also showed that Random Forests (RF) performed best in predicting the spatial
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distribution of SOC (RMSE=0.35% and R2 =0.60), compared to the other ML algorithms
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(i.e. Cubist: CU, k-Nearest Neighbor: kNN, Extreme Gradient Boosting: XGBoost and Support Vector Machines: SVM). Furthermore, results estimated the total SOC stocks
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(SOCS) for the whole study area (~15208 Tg) and amounts under different land uses.
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These were bareland (~6 Tg), orchard (~356 Tg), irrigated farming (~782 Tg), forest (~1773 Tg), grassland (~5991 Tg) and dry farming (~6297 Tg). As expected, the SOCS were highest in forest soils (652 g m-2 ) and lowest in bareland (437 g m-2 ). This result suggests that the conversion of native land (e.g. Forest) to cultivated land (e.g. Irrigated farming) could lead to significant loss of SOCS and appropriate management of land use could increase SOCS.
Keywords: Soil organic carbon stocks, machine learning algorithms, spatial prediction, random forests, land use, Aridisols 1.
Introduction
Journal Pre-proof Spatial information
about the
soil is
needed
increasingly
for making
informed
management decisions about the environment, particularly with regard to developing different types of agriculture, however, such information is often unavailable especially in western Iran (Nabiollahi et al., 2019). Soil is the largest terrestrial ecosystems sink of organic carbon and changes with atmospheric composition, climate, and land cover transformation. Soil organic carbon (SOC) is a key indicator of soil fertility and plays a
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vital role in the sequestration of CO2 and other greenhouse gases associated with global
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warming. Therefore, there is increasing demand for SOC information around the world
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(Schillaci et al., 2019; Yigini and Panagos, 2016). Evaluating SOC provides information
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about soil fertility, levels of sequestration of carbon, recovery of degraded soil, and the
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impact of land use change (Bonfatti et al., 2016).
Traditionally, soil property maps (including SOC maps) were created as polygon maps,
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with properties from representative soil profiles reported as the soil mapping units (Brus et al., 2017). These traditional SOC maps are costly and time-consuming to create and
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difficult to update. Also, traditional description, sampling and mapping of soil properties
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is unlikely to provide sufficient spatial resolution for the current uses that are being made of maps for ecosystem management. The variability of SOC is described by its relationships with environmental conditions (such as soil topography, climate, land use, vegetation, and soil type) or soil forming factors, that directly or indirectly affect the processes controlling the spatial distribution of SOC. Jenny(1994) explain soil development as a function of climate (c), organisms (o), relief (r), parent material (p), and time (a). This function was expanded by McBratney et al., (2003) to become the SCORPAN function. As a result, these environmental factors create a set of conditions that results in an increase or decrease in the amount of SOC.
Journal Pre-proof Thus SCORPAN factors are effective in predicting the spatial distribution of SOC in the Digital Soil Mapping (DSM). DSM has been developed to map spatial variability of soil properties with greater accuracy, economic efficiency and spatial resolution (Arrouays et al., 2014; McBratney et al. 2003). The relationships between soil and visible land surface properties, such as shape, position, and reflectance are used in DSM and traditional soil mapping, however,
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both methods take different approaches to all aspects of soil mapping, including project
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planning and preparation, sampling design, field operation, soil measurement, predictive
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modeling, and geographic representation (Roecker et al., 2010).
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A DSM is based on a statistical sampling in the field followed by laboratory analysis and
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mathematical prediction algorithms to create a spatial database of soil properties throughout the landscape, even areas that have not been sampled (Sanchez et al., 2009).
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DSM is spatially flexible for different soil properties and modelling can be done differently depending on project aims and available input data (Brus et al., 2017). DSMs
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are pixel-based and can be more easily shown at higher resolutions compared to
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traditional maps (Sanchez et al., 2009). DSM uses statistical and mathematical algorithms to predict and map soil attributes from easily obtained auxiliary variables (McBratney et al., 2003). Several machine learning (ML) algorithms have been used in DSM, including artificial neural networks (Li et al., 2013; Malone et al., 2009), support vector machines (Viscarra Rossel and Behrens, 2010), boosted regression trees (Martin et al., 2010), and random forests (Grimm et al., 2008; Vågen and Winowiecki, 2013; Wiesmeier et al., 2012). ML algorithms solve the problems of spatial autocorrelation, non-linearity in parametric and non-parametric statistical algorithms (Drake et al., 2006; Kuhn and Johnson, 2013; McRoberts, 2012; Padarian et al., 2019).
Journal Pre-proof In recent years, some researchers compared the performance of different machine learning algorithms for mapping SOC. For example, Somarathna et al., (2016) compared multiple linear regression, regression tree models, and support vector regression (SVR) for SOC mapping in Australia. Were et al., (2015) compared the performance of SVR, artificial neural network, and RF algorithms in Kenya. Due to the high variability in climate, soil properties, and land use management around the world, different algorithms have been
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used for DSM for different locations and variables (Kumar and Lal, 2011). Algorithms
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such as random forests (Hengl et al., 2018; Nabiollahi et al., 2019; Reza Pahlavan Rad et
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al., 2014), support vector regression (Ottoy et al., 2017; Were et al., 2015), XGBoost (Fan
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et al., 2018; Hengl et al., 2017; Meier et al., 2018) k-nearest neighbor (Mansuy et al.,
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2014; McRoberts, 2012), Cubist (Kidd et al., 2014; Taghizadeh-Mehrjardi et al., 2014; Viscarra Rossel et al., 2014) have all been used for DSM. In most SOC modeling studies,
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the RF and SVM models performed better.
Kurdistan province has extensive forests and pastures and can play a vital role in the
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discussions about carbon sequestration, but the distribution of SOC has not been
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investigated in Kurdistan using machine learning techniques. As there is a lack of information about the spatial variability of SOC in Iran, especially western Iran (Nabiollahi et al., 2019), the present study aims to evaluate the spatial distribution of SOC in Kurdistan province (29043 km2 ) located in western Iran using 865 soil samples, 101 covariates and 5 ML algorithms. In our study, we used a methodological structure to improve the prediction of SOC for the whole of Kurdistan province and determine how the environmental heterogeneity of Kurdistan influences the SOC distribution. The objectives of this study are to: (i) digitally map SOC with different ML algorithms, (ii) evaluate the effectiveness of models, (iii) identify the most important auxiliary variables controlling the spatial
Journal Pre-proof distribution of SOC in a semi-arid region and (iv) determine the spatial distribution of SOC and SOC stocks (SOCS) under different land uses. 2.
Materials and methods
2.1. Study area and soil data The study was conducted in Kurdistan province between latitudes of 34° 40ʹ and 36° 30ʹ North and longitudes of 45° 30ʹ and 48° 10ʹ 146.06° East (Figure 1a). This mountainous
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region of western Iran covers an area of 29043 km2 with elevations ranging from 720 to
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3240 m above sea level (Figure 2a). Its geographic position and climatic variability results
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in a wide range of biodiversity, with six main water sources (main rivers: Sirvan, Ghezel
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Ozan, Zarrinehroud, Siminrood, Razavar, Zab) and five main land uses (Figure 2b). Based
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on the Köppen method, the climate varies from dry to cool dry with a mean rainfall of 250 mm in the east to semi-humid with a mean rainfall of about 900 mm in the west of the
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province (Mozafari and Safarpour, 2013). The eastern and central regions of the province are affected by dry and warm weather with steppe vegetation cover and the western
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regions are affected by rainy weather and covered with Mediterranean, oak forests. The
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climate is classified as Csa (warm temperate- dry-hot summer), BSk (arid-steppe-cold arid) and Dsa (snow- dry- hot summer) in the Köppen-Geiger climate classification (http://koeppen-geiger.vu-wien.ac.at/present.htm) with a mean annual rainfall of 521 mm and mean annual temperature 12.38 °C. We used 865 soil data that were mainly produced by a Soil and Water Research Institute Project from 2000 to 2015. The plough layer of the soil was sampled (0-30 cm). The amount of SOC was determined by means of the wet oxidation with dichromate (Walkley and Black 1934).
Journal Pre-proof 2.2. Auxiliary variables Based on variables that can represent SCORPAN factors of soil development (McBratney et al., 2003) and review of literature (e.g. Bonfatti et al., 2016; Kumar and Lal, 2011; Kumar et al., 2012; Li et al., 2013; Liu et al., 2006; Schillaci et al., 2017; Shelukindo et al., 2014; Taghizadeh-Mehrjardi et al., 2016; Vasques et al., 2010), 101 auxiliary variables (predictors such as: remotely sensed attributes like Normalized Difference
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Vegetation Index, Soil Adjusted Vegetation Index etc.; terrain attributes like DEM,
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aspect, slope etc. and climate attributes like rain, air and soil temperature) were selected to
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explain the spatial variability of SOC. Three source databases were used: 1) the median
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values of atmospheric spectral bands of Landsat 5 TM obtained from 2000 to 2015, 2) a
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Digital elevation model (DEM) with a 30 m resolution and 3) climatic maps. Fifty-one auxiliary vegetation indices (see Appendix 1 for detailed information) were extracted
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from various band ratios (Mulder et al., 2011). Other band ratios were also calculated to represent parent material and soil factors in the study area (clay minerals, iron oxide,
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salinity index etc.). The terrain description of the area was performed using a freely
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downloadable DEM data (30 m resolution) obtained from http://srtm.csi.cgiar.org/. The pre-processed DEM was used to derive 47 terrain attributes using SAGA GIS (Conrad et al., 2015) and a brief description and reference to algorithms are given in Appendix 2. Climate data of annual average values of 30-year (1987–2017), i.e., mean annual temperature (AT, °C), mean annual rainfall (mm), and mean annual soil temperature (ST, °C)
were
recorded
at
10
weather
stations
in
Kurdistan
province
(http://kurdistanmet.telepol.ir) (Appendix 3); then to match them with the other raster grids they were interpolated in ARC GIS using the nearest neighbor method. All auxiliary variables obtained from the three source databases were aggregated (average resampling) or disaggregated (bilinear resampling) to a common grid of 90 × 90 m and
Journal Pre-proof then used as auxiliary variables for the development of quantitative spatial models. All of the data were in raster format and coordinates were converted to UTM WGS84 Zone 39 S. 2.3. Spatial prediction models Five supervised ML algorithms, Cubist: CU, k-Nearest Neighbor: kNN, Extreme Gradient Boosting: XGBoost, Support Vector Machines: SVM and Random Forest: RF, were used
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for SOC prediction. These algorithms are capable of modelling complex non-linear
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correlations between SOC and auxiliary variables. Further information and mathematical
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equations for all ML algorithms has been published by (Kuhn and Johnson, 2013).
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2.4.1 k-Nearest Neighbor
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The kNN- algorithm is a non-parametric approach to either univariate or multivariate prediction and classification (McRoberts, 2012) that is used to digitally map soil
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properties using environmental factors (Mansuy et al., 2014). The algorithms require no specific assumptions about the distribution of predictor variables, can use external
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information to the geographic area, and are suitable for map creation, small area
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estimation, and inference (McRoberts, 2012). The kNN construction is exclusively based on the samples from the training data, that are used to predict a new sample for regression, it classifies the kNNs samples in the predictor space using the mean of the K neighbor’s responses (Kuhn and Johnson, 2013). 2.4.2. Random forest RFs are a group of algorithms that have developed as an extension of Classification and Regression Tree analysis (CART) to enhance the prediction performance of the model (Breiman, 2001). RFs have been mainly used for classification problems (Boulesteix et al., 2012; Breiman, 2001; Olson et al., 2017). RFs are a data-driven statistical approach that has recently been employed in digital soil mapping studies (Akpa et al., 2016; Grimm
Journal Pre-proof et al., 2008; Hengl et al., 2018). Given that it shows good accuracy, is fast, simple to use, has useful internal estimation of error, and correlation and calculation of variable importance, this algorithm has been used to predict the spatial distribution of SOC recently (Grimm et al., 2008; Vågen et al., 2013; Wiesmeier et al., 2012). 2.4.3 Extreme Gradient Boosting The XGBoost algorithm is a simple tree-based algorithm which has recently become of
of
interest to DSM researchers (Fan et al., 2018). For instance, the XGBoost algorithm has
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been used to map soil nutrients (Hengl et al., 2017) and other soil properties (Meier et al.,
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2018; Ramcharan et al., 2018). Throughout the training phase in XGBoost, parallel
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calculations are automatically performed for the functions. The learning processes in the
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XGBoost are incremental, so that the first learner is linked to the input data space, and then the second model is applied to focus the weak learner's error. This correction process
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is repeated several times until the error criterion is eliminated. The final prediction of the model is obtained with the total prediction of each learner (Fan et al., 2018). It generates a
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weak learner at each step and accumulates it into the total model. If the weak learner for
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each step is based on the gradient direction of the loss function, it can be called Gradient Boosting Machines (GBM) (Friedman, 2002). Gradient tree boosting is one algorithm that has been used in many applications; and can give advanced results compared to many standard classification approaches (Fan et al., 2018). 2.4.4 Support vector machine The SVM is a class of effective, very flexible modeling algorithms. The theory behind it was initially
developed in the framework of classification models (Kuhn and Johnson,
2013). SVM analysis proposed by Cortes and Vapnik, (1995) is one of the general supervised ML tools for classification and regression. There are many planes in SVM to divide input data into different classes (Wang et al., 2018). Previous studies showed a
Journal Pre-proof better learning ability and lower prediction errors compared with many other algorithms (Maynard and Levi, 2017; Were et al., 2015). 2.4.5 Cubist The CU method is a combination of several algorithms and improves rule-based predictive models that balance the need for accurate prediction versus the requirements of intelligibility (Kuhn and Johnson, 2013). CU models are more commonly recognizable
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than neural networks and provide better results than those produced by simple algorithms
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such as multivariate linear regression (Kuhn et al., 2013; Viscarra Rossel et al., 2014). CU
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models have been designed to analyze big databases including hundreds of thousands to
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millions of records and tens to thousands of numeric or nominal fields (Kuhn and
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Johnson, 2013). The CU model prediction is based on linear regression models instead of separate values (Bui et al., 2009; Taghizadeh-Mehrjardi et al., 2014). Recently, the CU
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model has been used effectively in DSM in various countries (Kidd et al., 2014; Minasny et al., 2008; Viscarra Rossel et al., 2014).
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2.5 Validation of statistical algorithms
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We used 10 fold cross-validation with 100 replications to estimate the prediction performance of five models (Hengl et al., 2015). This algorithm provides a structure for creating numerous train/test splits in the dataset and certifying that each data point is in the test set at least once. It performs reliably and is unbiased for smaller data sets (Zeraatpisheh et al., 2019). To compare model performance, we use R2 , RMSE and MAE. (Gomez et al., 2008; Yang et al., 2015) described these measures of model performance as follows:
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where Pi and Oi are the predicted and observed SOC; n is the number of samples; 𝑃 and Ō are the means for the predicted and observed SOC. Models with the highest R2 and lowest RMSE and MAE were deemed the best models. The model calibration and validation were repeated using different auxiliary variables.
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2.6 SOCS measurement
which
is
a
derived
from
the
world
soil
database
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density
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The SOCS were calculated using predicted SOC, sampling depth (30 cm) and bulk
(ftp://ftp.soilgrids.org/data/recent/.) and calculated with the following equation.
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SOCS = [SOC × Ds × D]/100
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Where SOCS is soil organic carbon stocks (g m2 ), SOC is soil organic carbon concentrations (g kg), Ds is soil bulk density (Kg m3 ), and D is soil depth (m). Results and Discussion
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3.1 Descriptive statistics
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3.
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The descriptive statistics for SOC are given in Table 1. The results show that the mean SOC in the study area is 1.06 %. According to this table, the average SOC ranged from 0.04 to 4.44 % in the different types of land use. The difference between the minimum and maximum SOC is very high (4.4 %), this difference showed that the top soils are more easily affected by management, environmental variables and disturbance. The coefficient of variation (CV) for SOC was high (more than 51.04 %), which shows a wide range of values across the study area; it implies that the SOC has strong spatial dependence. Wilding (1985) classified CV values into 3 classes with high (CV > 35%), moderate (15%
Journal Pre-proof associated with the difference in land use, types of farming and management practices and topographic position in the study area. Falahatkar et al., (2016) also found this to be the case. Han et al., (2010) showed that soil properties such as SOC and pH are not independent but instead are stochastic variables promoted by the continuity of the soil forming processes and the change in the climate. Consequently, it is necessary to survey the spatial variability in SOC using modern statistical algorithms.
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Linear correlations between SOC and predictor variables are shown in Table 2. SOC at
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the soil surface is positively correlated with catchment slope (r=0.43 and negatively
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correlated with topographic wetness index (TWI) (r=-0.29) respectively. The correlation
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between climatic and topographic variables and the quantity of SOC has been documented
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previously (Garcia-Pausas et al., 2007). Climatic variables influence soil properties, vegetation cover, water retention, soil erosion and SOC decomposition. The effect of the
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rain (r=0.35) as a predictor is important. Aspect did not show a high correlation coefficient (r=0.04) with SOC in our study area. Falahatkar et al., (2016) and Zhao and
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Chen, (2005) also found this to be the case in their studies. The positive correlation of
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SOC with slope (r=0.35) in our study has been observed by Zhao and Chen, (2005) previously. Our results also indicated a negative correlation between SOC and the TWI, similar to the findings of Falahatkar et al., (2016) but contrary to the findings of Zhao and Chen, (2005) and Schwanghart and Jarmer, (2011). This negative result might have related to the great vegetation density with a small WI in the high elevation locations with less human activity (Falahatkar et al., 2016). The significant correlations of terrain variables with SOC (elevation r=- 0.46, slope r=- 0.43, and WI r=0.20 have been shown in the research of Li, (2010). The data were pre-processed to identify outliers before being used for SOC mapping. Outliers are data that have markedly higher or lower values than others in the dataset, and
Journal Pre-proof they can alter significantly the results of the statistical analysis. No such distributional outliers were found in the SOC data, and the relative normality of the data was confirmed (Figure 3). 3.2. Relative importance of covariates The relative importance of different variables for SOC prediction obtained by sensitivity analysis is shown in Figure 4. The most considerable positive contribution of any variable
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to SOC prediction was for rain (27.09 %). The importance of rain and other attributes
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could be related to the fact that SOC is highly affected by climate and topography in this
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study area. Western parts of this area have high precipitation and vegetative cover, while
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eastern parts have low precipitation and low vegetative cover. The RS indices were not
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recognized as the factors explaining a significant part of SOC variability in the study area. Similar to our results, Gomez et al., (2008) showed that the SOC content was not related
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to the RS indices and the SOC predictions were not influenced by the vegetation cover. All models showed rainfall as the most important variable for explaining the spatial
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variations of SOC. This was expected for statistical and theoretical reasons. Rainfall was
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categorized as the most significant variable that influenced the spatial distribution of SOC for a RF and boosted regression tree model at 0–30 cm (Wang et al., 2018). Similar to the results of our study, Davy and Koen, (2014) observed rainfall as the most important variable influencing SOCS in eastern Australia and Wang et al., (2018) showed that the relationship between climate variables (precipitation and temperature) and soil moisture, is a main driver of plant growth and net primary productivity, and therefore SOC dynamics. The effect of valley depth, terrain surface texture and catchment slope are complicated and maybe indirect. For example, there was an association between these attributes and climatic parameters such as precipitation and temperature, soil erosion and solar radiation.
Journal Pre-proof Previous results show that 71% of the SOC variability was described by terrain attributes (slope, aspect, slope gradient, curvature, WI, and proximity to the nearest stream) Thompson and Kolka, (2005) and others have documented that climate, land use, terrain and soil management control the spatial distribution of SOC (Adhikari et al., 2014; Guo et al., 2019; Minasny et al., 2013). The main terrain attributes which are usually used in SOC prediction and mapping across different scales are: elevation, slope, aspect,
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factor (Adhikari et al., 2014; Minasny et al., 2013).
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curvatures, wetness index, relative height and slope positions, MRVBF, MRRTF and LS
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For the study area, the results of sensitivity analysis indicated that elevation made a larger
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contribution to SOC prediction than the slope. The elevation might cause local variations
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in erosion, vegetation, management practice and sunlight which along with the chemical and physical composition of the organic matter are the major controllers of the
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decomposition and weathering of soil organic matter. Several studies have found different results with larger effects of aspect and slope than elevation (Falahatkar et al., 2016;
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Mendoza Vega, 2002; Yimer et al., 2006). Ayoubi et al., (2012) showed that SOC was
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lowest on steep slopes (more than 30%) that were affected by the highest soil erosion rates in western Iran. Falahatkar et al., (2016) showed that erosion and soil destruction decreased the SOC, yet several other researchers have shown a large correlation (r=0.74) between slope and SOCS (Liu et al., 2006; Tan et al., 2004; Yun-Qiang et al., 2009). 3.3. Performance of machine learning algorithms to predict SOC The results of the 10-fold cross-validation procedure used to compare the performance of kNN, RF, CU, XGBoost and SVM are summarized in Table 3. Based on the error indices (R2 , RMSE and ME), all models performed well, but RF was best. We found that there were slight differences between these models, suggesting that these six models were relatively stable in their predictive ability. The results showed that all models predicted
Journal Pre-proof SOC acceptably well based on the range of average values of R2 from 0.50 to 0.60; RMSEs between 0.35 and 0.42 and MAEs from 0.30 to 0.35. Results showed that the kNN algorithm could predict SOC with an R2 , RMSE and MAE of 0.50, 0.42 and 0.35, respectively. CU and SVM showed similar performance in predicting SOC, while XGBoost showed lower efficiency than the CU and SVM models in terms of R2 and prediction errors. The
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RF model showed that climate, vegetation indices and terrain attributes are important
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auxiliary variables for SOC prediction. Selecting appropriate values for SVR parameters
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is a main step in SVR analysis which has a great effect on its performance and the
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prediction accuracy for SOC (Hsu et al., 2007). Results show the performance of the SVR model for predicting SOC in the study area resulting from simulated algorithm analysis.
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The R2 , RMSE and MAE values for SOC predictions were 0.58, 0.36 and 0.3,
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respectively. These results are consistent with those of (Were et al., 2015). The RF model had the lowest RMSE (0.35) and MAE values, as well as the highest R2 (0.6) value.
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However, SVR and CU prediction had similar results with RMSE, MAE, and R2 values of
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0.36, 0.30, and 0.58, respectively. This showed quite different prediction accuracies for RF, CU and SVR.
Generally in DSM, model uncertainty may be due to differences in the amount of observed SOC or low predictor accuracy and modelling errors (Goidts et al., 2009; Yang et al., 2016). The increases in RMSEs for the RF, SVR, CU, XGBoost and kNN models can be seen in Table 3. The best model performances were selected for each model from ten-fold cross validation. Our results confirm that the RF and CU models are powerful ML algorithms for prediction, as reported by Akpa et al., (2016), Nawar and Mouazen, (2017), Wang et al., (2018), Zeraatpisheh et al., (2019) and Gomes et al., (2019).
Journal Pre-proof Prediction errors for SOC ranged from -0.24 to 0.19 (Figure 5) with areas where SOC was overestimated and underestimated being somewhat close together. The larger prediction errors were distributed throughout the study area and it can be concluded that the prediction error was related to the topography and vegetation of the area. Despite our expectation, the prediction error in the area with the lowest sample density is no more than area with the highest sample density.
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3.4. Spatial prediction of SOC
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Figure 6 shows the map of SOC obtained by the best model. The spatial patterns of SOC
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in all models are sensible with large values in the western part of the study area, which is
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dominated by forest and covered by dense vegetation, and small values in eastern areas
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with its calcareous soils and dry farming cultivation. The maps for all prediction models (not shown) showed both sharp and gradual changes across the study area. The highest
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SOC values occur in western Kurdistan province which is located in a semi-humid climate with a high mean rainfall, whereas the lowest SOC occurred in eastern areas
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where the arid-steppe-cold arid climate dominates. SOC concentrations are the result of
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the balance between inputs and outputs of carbon in soils; numerous factors influence this balance, according to environmental conditions (Davidson and Janssens, 2006) and local characteristics, such as vegetation (Jobbágy and Jackson, 2000) and topography (Tang et al., 2017). In our study precipitation and topography were the most important covariates driving the distribution of SOC, as shown by Gomes et al., (2019). These values are approximately twice the values of those for the dry biome (eastern part of the study area where the climate is drier and seasonal), where there is little accumulation of SOC. In the central area there is a greater relative accumulation of carbon due to high altitude, but less than under forest and more than eastern dry farming. 3.5. Spatial prediction of SOC stocks
Journal Pre-proof The spatial patterns of SOCS predicted by the RF model are shown in Figure 7. SOCS of the surface layer ranged from 187 to 1456 g m-2 . SOCS increased from east to west, with the highest stocks in the western, north and south-western areas. This showed the land cover effect because these were areas covered by grassland and forest. Furthermore, due to large above ground biomass, high rainfall, low temperatures, and higher altitudes, these areas provided favorable conditions for build-up of SOCS due to low SOC turnover at
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these locations. This has also been observed by Were et al., (2015), Wiesmeier et al.,
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(2012) and Smith, (2008). The lowest stocks were found in the eastern areas which
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included dry farming locations and grassland that had been converted to croplands. This
erosive processes (non-protective plowing,
non-rotational
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removal after harvesting,
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area had also experienced extensive erosion, and the low SOCS were due to biomass
farming and frequent tillage etc.), which breakdown the soil aggregates, changes aeration
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and increase the speed of microbial decomposition and oxidation of SOM to release CO2 (Dorji et al., 2014; Eclesia et al., 2012; Were et al., 2015). Dorji et al., (2014) found very
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similar variation in SOCS to those in this study area.
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3.6. SOC and SOCS under different land use Dorji et al., (2014) found, the spatial distribution of predicted SOCS under different land use types was quite similar to that of SOC. The highest and lowest SOCS were in the forest and bareland, respectively. The mean SOC and SOCS varied in soils under different land use types, and are shown in Table 4. The predicted SOCS for 90 × 90 m grids for the different land use types ranged from forest (651.83 g m-2 ) to bareland (437.16 31 g m-2 ) (Table 4). Taghizadeh-Mehrjardi et al., (2017), Were et al., (2015), Dorji et al., (2014) all found the same results. As expected, the spatial distribution of the predicted SOCS under different land use was quite similar to that of SOC. The highest SOC was found in forest (1.49 %) whereas bareland (0.95 %) and dry farming (1.09 %) soils had the lowest SOC
Journal Pre-proof (Table 4, Figure 8). Due to the high input of organic matter in forest and grassland, SOC was higher for native land than cropland. As expected, the variation in SOCS was very similar to SOC under all land uses. The mean SOC and SOCS showed an increasing trend from dry farming, irrigated farming, grassland, orchard and forest, respectively. This resulted from the management and related to disturbance activities in cultivated areas. We also estimated the total SOCS for the top 30 cm under different land use types. The
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total SOCS in soils in different land use types increased as follows: bareland (6.35 Tg; 1
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Tg= 1012 g), orchard (356.45 Tg), irrigated farming (782.38 Tg), forest (1773.79 Tg),
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grassland (5991.61 Tg) and dry land (6297.91 Tg) (Table 4).
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The total SOCS of the study area for the top 30 cm depth were 15209 Tg C (1 Tg=1012 g),
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indicating high SOC storage in the region, of which 41.4%, 39.4%, 11.7 %, 5.1%, 2.3% and 0.04% are in dry farming, grassland, forest, irrigated farming, orchard and bareland
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areas, respectively (Table 4). The difference in total SOCS between land use types is
4.
Conclusions
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generally due to the difference in area coverage in addition to their difference in SOC.
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This study shows that ML algorithms can be successfully used for mapping SOC and their uncertainty at a large scale in western Iran where there is a wide range in climate, land use and terrain attributes. Data quality can play important roles in the process. The procedural structure permits enhancement of the digital soil mapping process without loss of performance, selecting only the most important variables and the best model, and predicting the soil properties with the related uncertainty. The RF model showed the best performance in predicting SOC at the regional level, achieving the largest accuracy compared to the other ML algorithms tested. However, due to the similar performance of the RF, SVR, CU and XGBoost models, we suggest that all four models should be calibrated, and then the best results applied for spatial prediction of target soil attributes in
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The most important covariates that influence SOC
distribution in the Kurdistan region are rainfall, valley depth, terrain surface texture, protection index and air temperature. Grassland and forest areas of the western Kurdistan region have the greatest SOC and SOCS, showing the highest potential for carbon sequestration compared to cropland. Sustainable land management strategies and climate change mitigation in the area will need an understanding of the spatial distribution of
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SOCS; therefore, the SOCS map created here can identify areas for differential allocation
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of resources for carbon sequestration and fertility management. This type of information
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will be useful for evaluating the effect of land use change on total carbon cycling.
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5. Acknowledgments
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Financial support for this work was provided by Lorestn University. We thank the Kurdistan agricultural and natural resources research and education center and Dr. Sadri
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and Mr. Bostani for their intelligence and spiritual support. The work of Ruhollah Taghizadeh-Mehrjardi has been supported by the Alexander von Humboldt Foundation
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under the grant number: Ref 3.4 - 1164573 - IRN – GFHERMES-P.
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Figure 1. Location of Kurdistan province (study area) in Iran (a) and spatial distribution of soil
samples
(b).
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Figure 2. A digital elevation model (a) and Land use map of the study area (b)
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Figure 3. Histogram of SOC (%)
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Figure 4. Relative importance of environmental covariates (%) using the best prediction
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model (RF)
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Figure 5. Error map of predicted SOC (%) using RF model
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Figure 6. Spatial distribution of SOC (%) using the RF model
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Figure 7. Spatial distribution of total SOC stocks (g m-2 ) using RF model.
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Figure 8. SOC (%) in different land uses
Journal Pre-proof Table 1. Descriptive statistics of SOC (%) in the study area. No
Min
Me
Max
Med
SD
V
SE
CV
Quartile 25%
Quartile 75%
Kurtosis
Skewness
0.54
0.29
0.02
51.04
0.7
1.28
4.07
1.56
% 865
0.04
1.06
4.44
0.95
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Notes: No= Number of samples; Min= Minimum; Me= Mean; Max= Maximum; Med= Median; SD=Standard deviation; V= Variance; SE= Standard error; CV= Coefficient of variation.
Journal Pre-proof Table 2. Pearson correlation coefficients between SOC and environmental covariates. Parameter
SOC
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
SOC
1.00
0.43
0.42
0.41
0.37
0.35
0.33
0.32
0.30
0.28
0.10
-0.12
-0.18
-0.18
-0.18
-0.18
-0.20
-0.22
Catchment Slope
0.43
1.00
0.89
0.74
0.66
0.56
0.80
0.81
0.70
0.45
0.35
-0.34
-0.27
-0.28
-0.41
-0.34
-0.21
Protection Index
0.42
0.89
1.00
0.71
0.74
0.47
0.82
0.77
0.67
0.52
0.27
-0.22
-0.30
-0.31
-0.41
-0.37
Valley Depth
0.41
0.74
0.71
1.00
0.54
0.59
0.51
0.48
0.46
0.36
0.43
-0.56
-0.22
-0.34
T errain surface texture
0.37
0.66
0.74
0.54
1.00
0.38
0.60
0.61
0.33
0.61
0.11
-0.09
-0.32
-0.31
Rainfall
0.35
0.56
0.47
0.59
0.38
1.00
0.39
0.41
0.33
0.31
0.30
-0.51
-0.22
LS Factor
0.33
0.80
0.82
0.51
0.60
0.39
1.00
0.91
0.66
0.44
0.24
-0.12
f o
-0.24
Slope
0.32
0.81
0.77
0.48
0.61
0.41
0.91
1.00
0.68
0.38
0.22
19
X
-0.25
-0.29
-0.47
-0.48
-0.52
-0.57
-0.61
-0.27
-0.70
-0.51
-0.54
-0.56
-0.31
-0.25
-0.39
-0.35
-0.33
-0.63
-0.29
-0.38
-0.34
-0.44
-0.67
-0.73
-0.58
-0.21
-0.16
-0.21
-0.18
-0.20
-0.26
-0.32
-0.68
-0.27
-0.28
-0.31
-0.34
-0.19
-0.49
-0.52
-0.59
-0.43
-0.10
-0.25
-0.25
-0.29
-0.31
-0.18
-0.31
-0.59
-0.67
-0.47
Melton Ruggedness Number
0.30
0.70
0.67
0.46
0.33
0.33
0.66
0.68
1.00
0.20
-0.13
-0.18
-0.17
-0.30
-0.18
-0.13
-0.44
-0.30
-0.33
-0.37
Vector T errain Ruggedness (VRM)
0.28
0.45
0.52
0.36
0.61
0.31
0.44
0.38
0.16
0.21
-0.04
-0.22
-0.22
-0.14
-0.28
-0.19
-0.28
-0.35
-0.44
-0.33
Soil temp (20 cm)
0.10
0.35
0.27
0.43
0.11
0.30
0.24
0.22
0.20
0.21
1.00
-0.24
-0.11
-0.12
-0.05
-0.17
0.16
-0.06
-0.03
-0.06
-0.15
Dem
-0.12
-0.34
-0.22
-0.56
-0.09
-0.51
-0.12
-0.10
-0.13
-0.04
-0.24
1.00
-0.01
0.02
0.19
0.09
0.16
0.12
-0.01
-0.01
0.43
Band 1
-0.18
-0.27
-0.30
-0.22
-0.32
-0.22
-0.27
-0.25
-0.18
-0.22
-0.11
-0.01
1.00
0.95
0.10
0.85
0.13
0.16
0.25
0.28
0.29
Band 2
-0.18
-0.28
-0.31
-0.24
-0.31
-0.21
MRRT F
-0.18
-0.41
-0.41
-0.34
-0.29
Brightness
-0.18
-0.34
-0.37
-0.31
-0.38
Flow Path Length (downstream)
-0.20
-0.21
-0.27
-0.25
-0.34
rn
-0.28
-0.25
-0.17
-0.22
-0.12
0.02
0.95
1.00
0.13
0.93
0.13
0.17
0.23
0.27
0.27
-0.31
-0.29
-0.30
-0.14
-0.05
0.19
0.10
0.13
1.00
0.15
0.10
0.31
0.09
0.17
0.23
-0.21
-0.34
-0.31
-0.18
-0.28
-0.17
0.09
0.85
0.93
0.15
1.00
0.14
0.18
0.29
0.34
0.31
-0.18
-0.19
-0.18
-0.13
-0.19
0.16
0.16
0.13
0.13
0.10
0.14
1.00
0.18
0.23
0.25
0.29
Downslope Curvature
-0.22
-0.48
-0.70
-0.39
-0.44
-0.20
-0.49
-0.31
-0.44
-0.28
-0.06
0.12
0.16
0.17
0.31
0.18
0.18
1.00
0.17
0.12
0.28
MRVBF
-0.25
-0.52
-0.51
-0.35
-0.67
-0.26
-0.52
-0.59
-0.30
-0.35
-0.03
-0.01
0.25
0.23
0.09
0.29
0.23
0.17
1.00
0.82
0.43
T opographic Wetness Index
-0.29
-0.57
-0.54
-0.33
-0.73
-0.32
-0.59
-0.67
-0.33
-0.44
-0.06
-0.01
0.28
0.27
0.17
0.34
0.25
0.12
0.82
1.00
0.49
u o
J
-0.16
l a
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e
o r p
0.16 1.00
18
Journal Pre-proof Table 3. Performance of five different modeling methods to predict SOC R2 0.50 0.60 0.58 0.57 0.58
RMSE (%) 0.42 0.35 0.36 0.37 0.36
MAE (%) 0.35 0.30 0.30 0.31 0.30
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Model kNN RF Cu XGBoost SVR
Journal Pre-proof Table 4. Statistical description of SOC and SOCS in each land use type.
of ro -p re lP na ur
Forest Orchard Grassland Irrigated farming Dry farming Bareland
Min 0.64 0.45 0.53 0.42 0.41 0.66
SOCS (g m-2 ) Max Mean 1455.76 651.83 1123.00 554.31 1123.13 544.53 1019.18 499.00 1254.65 486.91 718.90 437.16
SOC (%) Max Mean Stdev Min 3.27 1.49 0.17 400.80 2.65 1.27 0.35 243.81 2.62 1.23 0.26 248.45 2.67 1.12 0.31 192.99 2.81 1.09 0.28 186.66 1.66 0.95 0.24 321.30
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Land use
Stdev 76.434 139.90 106.08 134.63 116.69 104.84
total SOCS Tg 1773.79 356.46 5991.61 782.38 6297.91 6.35
Journal Pre-proof Appendix 1. Remotely sensed attributes used in the prediction of SOC and SOCS in the study area. Reference Taghizade et al (2016a) Taghizade et al (2016a) Taghizade et al (2016a) Taghizade et al (2016a) Taghizade et al (2016a) Taghizade et al (2016a) Taghizade et al (2016a) Taghizade et al (2016a) Welikhe et al (2017) P ettorelli et al (2005) P ettorelli et al (2005) Arzani and King (2008) P ettorelli et al (2005) Ghaemi et al (2013) Arzani and King (2008) Arzani and King (2008) Arzani and King (2008) Arzani and King (2008) Ghaemi et al (2013) Ghaemi et al (2013) Kure ar al (2015) Foody et al (2001) Foody et al (2001) Foody et al (2001) Taghizade et al (2016a)
(Band4- Band2/ Band4+ Band2)
Gitelson et al (1996)
(Band4/ Band3+ Band4) (Band4- Band5/ Band4+ Band5)
Crippen (1990) Sriwongsitanon et al (2016)
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Formula Reflectance value of band 1 (blue visible) (band width=0.45 –0.515 μm) Reflectance value of band 2 (green visible) (band width=0.525 –0.605 μm) Reflectance value of band 3 (red visible) (band width=0.63 –0.69 μm) Reflectance value of band 4 (near infrared) (band wi dth=0.75–0.90 μm) Reflectance value of band 5 (shortwave IR-1) (band width=1.55–1.75 μm) Reflectance value of band 6 (thermal band) (band width=10.4 –12.5 μm) Reflectance value of band 7 (shortwave IR-2) (band width=2.09–2.35 μm) (Band4-Band3/Band4+Band3) (Band5/Band4) (Band5/Band7) (Band5- Band3/ Band5+ Band3) (Band4/( Band3+ Band5)) (Band4/ Band3) (Band7- Band5/ Band7+ Band5) (Band3- Band1) (Band3- Band2) ((Band3- Band2)/( Band3+ Band2)) ((Band3- Band1)/(Band3+ Band1)) ((Band7- Band3/(Band7+ Band3)) (Band4- Band3) (Band3- Band4/ Band3+ Band4) (Band4/ Band1+ Band2) (Band1* Band2)/ Band3 ((Band4-( Band1+ Band2)/( Band4+( Band1+ Band2))) (Band4/ Band3)
Lymburner et al (2000)
(Band5- Band2) (Band5- Band2/ Band5+ Band2) (Band4- Band3)/((Band4+ Band3)^1/2) (0.29 Band2-0.56 Band3+0.6 Band5+0.49 Band2) (2.5*( Band4- Band3)/( Band4+6* Band3-7.7* Band1+1) ((Band1^2+ Band2^2+ Band3^2)/3)^0.5 (Band3- Band1/ Band3+ Band1) (2*( Band3- Band2- Band1))/( Band2- Band1) (Band3- Band2/ Band3+ Band2) (Band3^2/ Band1* Band2) (Band5/ Band7) (Band4- Band5/ Band4+ Band5) (Band5/ Band7) (Band3/ Band1) (Band5/ Band4) (Band5- Band6/ Band3+ Band6) (Band5- Band7/ Band5+ Band7 (Band7- Band6/ Band7+ Band6) (Band5- Band6/ Band5+ Band6) (Band3- Band6/ Band3+ Band6) ((Band4-(1.2* Band3))/ Band4+ Band3
Vescovo and Gianelle (2008) Vescovo and Gianelle (2008) Roujean and Breon (1995) Ghaemi et al (2013) Wang et al (2018) Escadafal et al (1994) Escadafal and Huete (1991) Escadafal and Huete (1991) Madeira at al (1997) Madeira at al (1997) Goodwin et al (2008) Goodwin et al (2008) Dogan (2009) Dogan (2009) Dogan (2009)
(Band4- Band3/ Band4+ Band3+0.5)*(1+0.5))
Taghizade et al (2016a)
(Band4- Band3/ Band4+ Band3+0.16)
Nikolakopoulos )2003)
(Band4- Band5/ Band4+ Band5) (0.3037* Band1)+(0.2793* Band2)+(0.4343* Band3)+ (0.5585* Band4)+(0.5082* Band5)+(0.1863* Band7) (-0.2848* Band1)+(-0.2435* Band2)+ (-0.5436* Band3)+(0.7243* Band4)+(0.084* Band5)+(-0.18* Band7) (-0.1509* Band1)+(-0.1793* Band2)+(-0.3299* Band3)+ (0.3406* Band4)+(-0.7112* Band5)+(-0.4572* Band7)
Wang et al (2018)
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(Band4/ Band3+ Band5)
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P arameters Band 1 Band 2 Band 3 Band 4 Band 5 Band 6 Band 7 Normalized Difference Vegetation Index (NDVI) Moisture Stress Index (MSI) Leaf Water Content (LWC) Transformed Vegetation Index (TVI) reflectance absorption index (RAI) Near Infrared Ratio (NIR) Vegetation Index (VI) P D311 P D321 P D322 P D312 MIRV1 Difference Vegetation Index (DVI) Normalized Difference Snow Index (NDSI) Ratio-based (RB) Stress Related (SR) Normalized based (NB) Ratio Vegetation Index (RVI) Green Normalized Difference Vegetation Index (GNDVI) Infrared P ercentage Vegetation Index (IP VI) Normalized Difference Infrared Index (NDII) Specific Leaf Area Vegetation Index (SLAVI) Canopy Index (CI) Normalized Canopy Index (NCI ) Renormalized difference vegetation index (RDVI ) Green vegetation index (GVI) Enhanced vegetation index (EVI) Brightness Index (BI) Saturation Index (SI) Hue Index (HI) Coloration Index (CoI) Redness Index (RE) Moisture Index (MI) Normalized Difference Water Index (NDWI) Clay Minerals (CM) Iron Oxide (IO) Ferrous Minerals (FM) Chemical soil composition (CSC) salinity index (S-I) Normalized Difference Bareness Index (NDBA11) Normalized Difference Bareness Index (NDBA12) Normalized Difference Bareness Index (NDBA13) Modified Normalized Difference (MND) Soil Adjusted Vegetation Index (SAVI) Optimized Soil Adjusted Vegetation Index (OSAVI) Normalized difference moisture index (NDMI) Tasseled cap coefficient (brightness) Tasseled cap coefficient (greenness) Tasseled cap coefficient (wetness)
Taghizade et al (2016a) Zhao and Chen (2005) Zhao and Chen (2005) Zhao and Chen (2005) P ettorelli et al (2005)
Huang et al. (2002) Huang et al. (2002) Huang et al. (2002)
Journal Pre-proof Appendix 2. Terrain attributes used in the prediction of SOC and SOCS in the study area
T opographic position index Normalized height Standardized height Mid-slope position Landform
T errain Surface Convexity T errain Surface T exture Local curvature Upslope curvature Local Upslope curvature Downslope curvature Local Downslope curvature Wind effect
T aghizade et al (2016a)
of
Bonfatti et al (2016) Bonfatti et al (2016) Bonfatti et al (2016) Guo et al (2019) Guo et al (2019) T aghizade et al (2016a) Wilson and Gallant (2000) T aghizade et al (2016d)
T aghizade et al (2016a)
Balance between soil mass deposited and eroded Measures terrain ruggedness Angle between the surface and the incoming light beams Calculates the vertical distance to a channel network base level
Bonfatti et Bonfatti et Bonfatti et Bonfatti et
Simple flow accumulation related index, calculated as difference between maximum and minimum elevation in catchment area divided by square root of catchment area size. T he calculation is performed for each grid cell, therefore minimum elevation is same as elevation at cell's position
Melton (1965)
al (2016) al (2016) al (2016) al (2016)
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Flow path lenght Upslope length factor Effective flow length Sediment balance Curvature classification Slope height Morphometric features Protection index
Identifies valley bottoms based on their topographic signature as flat low-lying areas, Measure of flatness and up-ness Measure of flatness and low-ness, Identifies high flat areas
T aghizade et al (2016a)
na
Catchment Area Catchment Slope Modified Catchment Area Slope length Multi-resolution valley bottom flatness index Multi-resolution ridge-top flatness index Mass Balance Index Vector T errain Ruggedness Analytical Hillshading Vertical Distance to Channel Network Maximum height Melton ruggedness number
Guo et al (2019)
ro
Relative Slope Position
Represents the agreement of the aspect direction of surrounding cells with the theoretical matrix direction. It is calculated as the mean aspect difference between the real aspect and the theoretical maximum divergent direction matrix which is the ideal peak minus 90°. Calculates accumulated flow as the accumulated weight of all cells flowing into each downslope cell in the output raster T opographic wetness index Slope length factor Relative position of the valley Defined as the elevation difference between the cell and the closest channel network defined as the position of one point relative to the ridge and valley of a slope, with a value of 0 for the bottom of the valley and 1 for the top of the ridge Calculated flow accumulation and related parameters Average slope over the catchment Calculated the flow accumulation
T aghizade et al (2016a) T aghizade et al (2016a) Schillaci et al (2017)
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T opographicWetness Index Ls Factor Valley Depth Chanell network base level
Reference
re
Flow Accumulation
Data descriptions Elevation above mean sea level Average gradient above flow path Compass direction of the maximum rate of change
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Variables DEM- 30 m Slope Aspect Cross-Sectional Curvature Longitudainal Curvature Convergence Index
T his algorithm analyses the immediate surroundings of each cell up to an given distance and evaluates how the relief protects it T his implementation calculates the TPI for different scales and integrates these into one single grid Normalized height of elevation is defined by slope height and valley depth Standard height is the product of normalized height multiplied by absolute height
Guisan et al (1999) Guo et al (2019) Guo et al (2019)
T he obtained landform classification map successfully shows the distribution of plains, peaks and steep slopes. Attributes used for the classification were elevation, slope, plan curvature, profile curvature, tangential curvature and both maximal and minimal curvature. T he convexity is calculated as the ratio of the number of cells having positive curvature to the number of all valid cells within the specified search radius. T errain surface texture calculates the nested-means terrain classification Calculates the local curvature of a cell as sum of the gradients to its neighbour cells. Upslope curvature is the distance weighted average local curvature in a cell's upslope contributing area based on multiple flow direction after Freeman 1994.
Guisan et al (1999)
T he Wind Effect is a dimensionless index. Values below 1 indicate wind shadowed areas whereas values above 1 indicate areas exposed to wind
Boehner and Antonic (2009)
Iwahashi and Pike (2007) Freeman (1991)
Journal Pre-proof
Appendix 3. Climate attributes used in the prediction of SOC and SOCS in the study area. Description Mean annual temperature Mean annual soil temperature in 20-cm Mean annual rainfall
Reference Wang et al (2018) Wang et al (2018)
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P arameters Air temperature (AT) Soil temperature (ST) Rainfall
Journal Pre-proof
Highlights
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Spatial distribution of SOC in western Iran at a fine resolution was predicted. Different machine learning algorithms were compared. SOC stocks was assessed in different land uses.
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