# Estimation of Organic Carbon in Anthropogenic Soil by VIS-NIR Spectroscopy: Effect of Variable Selection

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## Abstract

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## 1. Introduction

^{2}[24]. It is not enough to reveal the heterogeneous relationship between the VIS-NIR spectra and SOC on a small scale [25]. Therefore, many researchers made efforts on small-scale studies with soil samples collected from farmland, when VIS-NIR spectroscopy showed good performance [26,27,28,29,30]. These farmlands are continuous and have a large area with similar human activities. However, the heterogeneity in the relationship between SOC and VIS-NIR spectra is more complex in the highly fragmented farmland with various human activities, which can weaken the performance of the SOC estimation model by VIS-NIR spectra. To improve model performance, previous studies adopted the strategy of using representative calibration samples [26,27,28,29]. Nevertheless, the efficiency of this strategy is susceptible to sample size [30]. Therefore, it is essential to investigate other approaches that may improve model accuracy. Besides, VIS-NIR spectra featured by high spectral resolution may contain abundant spectral information, which may complicate the SOC estimation models [31,32]. Thus, it is necessary to establish new approaches to improve model parsimony.

## 2. Materials and Methods

#### 2.1. Sampling Area and Soil Samples

^{2}[53]. The geographical coordinates of these samples were recorded by a hand-held global positioning system, and the geographical distributions are shown in Figure 1. The total collected soil samples (Dataset 0) were divided into three datasets according to sampling locations, land use and land cover types (Dataset 1, Dataset 2, and Dataset 3, respectively). Samples of the three datasets were collected from three sites with different human activities on a small scale [18]. Samples of Dataset 1 was collected from cropland that was adjacent to a breeding pond. Dataset 2 was sampled from cropland that was surrounded by cropland. Dataset 3 included samples of various land-use types (cropland, artificial forest, meadows, and breeding ponds). These samples were put in sealed plastic bags with sampling sequence labels and then were sent to the laboratory at room temperature on 22 December 2011. After a principle components analysis and a 3σ standard, five outliers were discarded, and 103 samples were retained for further data analysis in this study.

#### 2.2. VIS-NIR Spectral Measurement and SOC Analysis

#### 2.3. Spectral Pretreatment

#### 2.4. Spectral Variable Selection

_{cv}) with the retained variables as a new variable subset; (4) repeat steps 1–3 for N runs to obtain N new variable subsets; and (5) choose the new subsets with the lowest RMSE

_{cv}as the optimal variable subset [41]. The run times (N) was set to 50 in this study.

_{cv}; and (5) choose the variable subset with the lowest RMSE

_{cv}as the optimal variable subset. X (m×n), Y (n×1), N, and Q are the key input parameters for this algorithm, where X is the spectral variables, and Y is the SOC content, in which m is the number of samples, and n is the number of spectral variables. N is the number of iterations, and Q is the number of variables consisting of the initialized variable subset [44]. The number of iterations (N) was set to 50 in this study. In this study, CARS and RF were performed in Matlab (R2018b, MathWorks, Inc., Natick, MA, USA) with the libPLS toolbox (Version 1.98), which was available at http://www.libpls.net/download.php.

#### 2.5. Model Calibration and Validation

^{2}), the root mean squared error (RMSE) and the residual prediction deviation (RPD) were calculated using Equations (1)–(3) [57]. A desirable PLSR estimation model should have high R

^{2}and RPD with a low RMSE on the validation dataset.

## 3. Results

#### 3.1. Statistical Description of Soil Samples

#### 3.2. Raw Spectra and Pretreated Spectra

#### 3.3. Correlation Analysis

#### 3.4. Spectral Variable Selection

_{cv}for spectra with different pretreatments (e.g., 25, 23, 25, 25, and 28 for the pretreatments of None, FD, MC, MSC, and SNV, respectively).

_{cv}in different spectral variable selection probability. Spectral variables were selected as the optimal subset with the lowest 5-Flod RMSE

_{cv}. According to Figure 7, RMSE

_{cv}had minimum values when the probability was 0.8, 0.8, 0.3, 0, 0.4, and 0.5 for the spectral pretreatments of None, FD, Log (1/R), MC, MSC, and SNV, respectively.

#### 3.5. Accuracy of Estimation after Different Pretreatment and Variable Selection Techniques

_{p}

^{2}in each spectral variable selection category slightly increased from 0.80 (Full spectrum) to 0.81 (CARS) and 0.83 (RF), and RPD increased from 1.96 (Full spectra) to 2.05 (CARS) and 2.11 (RF).

_{p}

^{2}increased from 0.70 to 0.80; RMSE

_{p}decreased from 3.60 g/kg to 3.17 g/kg; and RPD increased from 1.72 to 1.96. MSC and SNV had negative effects, as R

_{p}

^{2}remained 0.70; RMSE

_{p}increased from 3.60 g/kg to 3.66 g/kg; and RPD decreased from 1.72 to 1.69. Full-spectrum PLSR model with FD had the largest RPD difference (0.23), and that with MSC and SNV had the lowest RPD difference (−0.03).

_{p}

^{2}, RMSE

_{p}and RPD values were 0.81, 3.02 g/kg and 2.05, respectively. The worst R

_{p}

^{2}, RMSE

_{p}and RPD values were 0.73, 3.42 g/kg and 1.81, respectively. CARS + PLSR model with MSC had the largest RPD difference (−0.25), and that with MC had the lowest RPD difference (0.01).

_{p}

^{2}increased from 0.72 to 0.83; RMSE

_{p}decreased from 3.34 g/kg to 2.94 g/kg; and RPD increased from 1.86 to 2.11. The RF + PLSR model with Log (1/R) had the largest RPD difference (0.23), and that with SNV had the lowest RPD difference (−0.03).

_{p}

^{2}= 0.81, RMSE

_{p}= 3.02 g/kg, and RPD = 2.05, Log (1/R) + RF + PLSR model: R

_{p}

^{2}= 0.83, RMSE

_{p}= 2.94 g/kg, and RPD = 2.11).

## 4. Discussion

#### 4.1. The Effect of Spectral Variable Selection Techniques on Model Accuracy

^{2}= 0.80, RPD = 1.96 and $\overline{\mathrm{RPD}}$ = 1.81; with spectral variable selection: the best R

^{2}= 0.83, RPD = 2.11 and $\overline{\mathrm{RPD}}$ = 1.94). This is because that spectral variable selection could eliminate unimportant information, reserve relevant information, and reduce spectral collinearity [37]. The performance of the proposed spectral variable selection was comparable to other strategies that aimed to improve the accuracy of PLSR models for anthropogenic soil. Liu et al. compared a variety of sample selection algorithms, which aimed to develop a representative calibration dataset for SOM estimation [18]. The best RPD achieved in their study was lower than the $\overline{\mathrm{RPD}}$ in this study. Liu et al. further combined the Kennard–Stone algorithm and spectral pretreatment to choose representative calibration samples, and achieved an $\overline{\mathrm{RPD}}$ of 1.85, which was still poorer than that obtained in the current study [59]. Wang et al. proposed the MVARC-R-KS method to select representative calibration samples (not spectral variables as in the current study), which has resulted in good accuracy of PLSR models [61]. They reported that the best RPD was 1.81, which was also lower than the $\overline{\mathrm{RPD}}$ in this study. These mentioned strategies mainly focus on the selection of representative calibration samples to improve the accuracy of PLSR models, while our strategies focus on the selection of representative spectral variables. A combination of these two strategies to further improve the performance of PLSR models in SOC estimation could be explored in future rese arch.

#### 4.2. The Effect of Spectral Variable Selection Techniques on Model Parsimony

#### 4.3. The Implication of the Proposed Strategy

^{2}= 0.83 and RPD = 2.05; CARS: R

^{2}= 0.81, and RPD = 2.11).

## 5. Conclusions

^{2}= 0.83, RPD = 2.11, and the number of spectral variables = 83; the best models with CARS: R

^{2}= 0.81, RPD = 2.05, and the number of spectral variables = 31); (iii) the effects of spectral pretreatments vary among spectral variable selection algorithms. All FD, Log (1/R), MC, MSC, and SNV could improve the accuracy of PLSR models with RF, whereas only Log (1/R) and MC could slightly improve the accuracy of PLSR models with CARS; and (iv) appropriate number and distribution of spectral variables could be selected by Log (1/R) after both CARS and RF.

## Author Contributions

## Funding

## Acknowledgments

## Conflicts of Interest

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**Figure 2.**The raw and pretreated soil spectra. (

**a**) None: raw spectra; (

**b**) FD: the spectra after first derivative; (

**c**) Log (1/R): the absorption spectra; (

**d**) MC: the spectra after mean centering; (

**e**) MSC: the spectra after multiplicative scatter correction; and (

**f**) SNV: the spectra after standard normal variate.

**Figure 3.**Correlation coefficient curves calculated between the raw visible and near-infrared (VIS-NIR) spectra and soil organic carbon (SOC) for four datasets. The blue line, green line, red line, and magenta line refer to correlation coefficient curves for Dataset 1, Dataset 2, Dataset 3, and Dataset 0, respectively. The blue ‘+’, green ‘+’, and magenta ‘+’ symbols refer to locations of VIS-NIR spectral variables having significant correlation for Dataset 1, Dataset 2, and Dataset 0, respectively (at a significance level of 0.05). The ‘◆’ symbol refers to the location of spectral variables having the lowest correlation coefficient.

**Figure 4.**Competitive adaptive reweighted sampling (CARS) variable selection of Log (1/R) spectra: (

**a**) the number of sampled variables; (

**b**) 5-Fold root mean squared error of cross-validation (RMSE

_{cv}) values; and (

**c**) regression coefficient path of each spectral variable during the 50 iterations.

**Figure 5.**The distributions of spectral variables selected by competitive adaptive reweighted sampling (CARS) with different spectral pretreatments.

**Figure 6.**Spectral variables selection probability by Random Frog (RF) with different spectral pretreatments. (

**a**) probability without pretreatment; (

**b**) probability with first derivative (FD); (

**c**) probability with Log (1/R); (

**d**) probability with mean centering (MC); (

**e**) probability with multiplicative scatter correction (MSC); and (

**f**) probability with standard normal variate (SNV).

**Figure 7.**Five-fold root mean square error of cross-validation (RMSE

_{cv}) for different spectral variable selection probability by Random Frog (RF) shown for different spectral pretreatments.

**Figure 8.**The distributions of spectral variables selected by Random Frog (RF) with different spectral pretreatments.

**Figure 9.**(

**a**) Ratio of prediction deviation (RPD) difference between competitive adaptive reweighted sampling (CARS)/random frog (RF) and full spectrum SOC models after the same spectral pretreatments (spectral pretreatments include non-pretreatment (None), first derivative (FD), Log (1/R), mean centering (MC), multiplicative scatter correction (MSC), and standard normal variate (SNV)); (

**b**) RPD difference between non-pretreated and pretreated SOC models after the same variable selection algorithms (variable selection algorithms include full spectrum, CARS, and RF).

Samples | N ^{a} | SOC (g/kg) | SD ^{d} | CV ^{e} | CS ^{f} | CK ^{g} | ||
---|---|---|---|---|---|---|---|---|

Min ^{b} | Max ^{c} | Mean | ||||||

Total | 103 | 2.35 | 33.95 | 16.05 | 6.35 | 40% | −0.04 | 2.32 |

Calibration | 69 | 2.35 | 33.95 | 16.14 | 6.46 | 40% | 0.04 | 2.46 |

Validation | 34 | 3.30 | 26.23 | 15.85 | 6.20 | 39% | −0.23 | 1.93 |

^{a}Sample numbers;

^{b}Minimum;

^{c}Maximum;

^{d}Standard deviation;

^{e}Coefficient of variation;

^{f}Coefficient of skewness;

^{g}Coefficient of kurtosis.

**Table 2.**Accuracies of soil organic carbon (SOC) estimation using full-spectrum-based partial least squares regression (PLSR) models, competitive adaptive reweighted sampling (CARS)-based PLSR models, and random frog (RF)-based PLSR models after different spectral pretreatments.

Spectral Variable Selection | Spectral Pretreatments | N ^{a} | LVs ^{b} | Calibration Dataset | Validation Dataset | RPD | $\overline{\mathbf{R}\mathbf{P}\mathbf{D}}{\text{}}^{\mathbf{c}}$ | ||
---|---|---|---|---|---|---|---|---|---|

R_{c}^{2} | RMSE_{c} | R_{p}^{2} | RMSE_{p} | ||||||

Full Spectra | None | 205 | 9 | 0.79 | 2.93 | 0.70 | 3.60 | 1.72 | 1.81 |

FD | 205 | 7 | 0.78 | 3.01 | 0.80 | 3.17 | 1.96 | ||

Log(1/R) | 205 | 11 | 0.86 | 2.44 | 0.76 | 3.37 | 1.84 | ||

MC | 205 | 10 | 0.86 | 2.36 | 0.75 | 3.24 | 1.92 | ||

MSC | 205 | 8 | 0.78 | 3.02 | 0.70 | 3.66 | 1.70 | ||

SNV | 205 | 8 | 0.78 | 3.02 | 0.70 | 3.66 | 1.69 | ||

CARS | None | 21 | 8 | 0.85 | 2.45 | 0.78 | 3.05 | 2.03 | 1.94 |

FD | 26 | 7 | 0.85 | 2.44 | 0.73 | 3.42 | 1.81 | ||

Log(1/R) | 31 | 8 | 0.84 | 2.53 | 0.81 | 3.02 | 2.05 | ||

MC | 21 | 8 | 0.87 | 2.35 | 0.78 | 3.04 | 2.04 | ||

MSC | 21 | 6 | 0.79 | 2.91 | 0.77 | 3.49 | 1.78 | ||

SNV | 16 | 6 | 0.83 | 2.66 | 0.77 | 3.23 | 1.92 | ||

RF | None | 39 | 10 | 0.83 | 2.61 | 0.72 | 3.34 | 1.86 | 1.94 |

FD | 21 | 14 | 0.84 | 2.53 | 0.76 | 3.14 | 1.97 | ||

Log(1/R) | 83 | 11 | 0.86 | 2.42 | 0.83 | 2.94 | 2.11 | ||

MC | 101 | 10 | 0.85 | 2.45 | 0.77 | 3.18 | 1.95 | ||

MSC | 106 | 11 | 0.89 | 2.16 | 0.76 | 3.28 | 1.89 | ||

SNV | 63 | 8 | 0.81 | 2.83 | 0.77 | 3.31 | 1.87 |

^{a}Number of selected spectral variables;

^{b}Number of latent variables;

^{c}Mean of ratio of prediction deviation (RPD).

Locations of Selected Spectral Variables (nm) | Possible Fundamental Bonds | Possible Wavelength (nm) | Possible Related Soil Constituents |
---|---|---|---|

800 | C–H | 825 | Organics (aromatics) |

1000 | N–H | 1000 | Organics (amine) |

1100 | C–H | 1100 | Organics (aromatics) |

1200 | C–H | 1170 | Organics (Alkyl asymmetric-symmetric doublet) |

1420 | O–H | 1380 | Water |

1500 | C–O | 1524 | Organics (amides) |

1800 | C–H | 1754 | Organics (Alkyl asymmetric-symmetric doublet) |

1920 | O–H | 1915 | Water |

2000 | C–O | 2033 | Organics (amides) |

2100 | N–H | 2060 | Organics (amine) |

2200 | Al–OH | 2230 | Clay minerals |

2350 | C–O | 2381 | Organics (Carbohydrates) |

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## Share and Cite

**MDPI and ACS Style**

Xu, L.; Hong, Y.; Wei, Y.; Guo, L.; Shi, T.; Liu, Y.; Jiang, Q.; Fei, T.; Liu, Y.; Mouazen, A.M.; Chen, Y. Estimation of Organic Carbon in Anthropogenic Soil by VIS-NIR Spectroscopy: Effect of Variable Selection. *Remote Sens.* **2020**, *12*, 3394.
https://doi.org/10.3390/rs12203394

**AMA Style**

Xu L, Hong Y, Wei Y, Guo L, Shi T, Liu Y, Jiang Q, Fei T, Liu Y, Mouazen AM, Chen Y. Estimation of Organic Carbon in Anthropogenic Soil by VIS-NIR Spectroscopy: Effect of Variable Selection. *Remote Sensing*. 2020; 12(20):3394.
https://doi.org/10.3390/rs12203394

**Chicago/Turabian Style**

Xu, Lu, Yongsheng Hong, Yu Wei, Long Guo, Tiezhu Shi, Yi Liu, Qinghu Jiang, Teng Fei, Yaolin Liu, Abdul M. Mouazen, and Yiyun Chen. 2020. "Estimation of Organic Carbon in Anthropogenic Soil by VIS-NIR Spectroscopy: Effect of Variable Selection" *Remote Sensing* 12, no. 20: 3394.
https://doi.org/10.3390/rs12203394