Articles | Volume 6, issue 2
https://doi.org/10.5194/soil-6-565-2020
© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/soil-6-565-2020
© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Original research article
| 
17 Nov 2020
Original research article |
| 17 Nov 2020
| 17 Nov 2020
The influence of training sample size on the accuracy of deep learning models for the prediction of soil properties with near-infrared spectroscopy data
School of Life and Environmental Sciences and Sydney Institute of
Agriculture, The University of Sydney, NSW, Australia
Budiman Minasny
School of Life and Environmental Sciences and Sydney Institute of
Agriculture, The University of Sydney, NSW, Australia
Wanderson de Sousa Mendes
Department of Soil Science, Luiz de Queiroz College of
Agriculture, University of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
José Alexandre Melo Demattê
Department of Soil Science, Luiz de Queiroz College of
Agriculture, University of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
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Wartini Ng, Budiman Minasny, Alex McBratney, Patrice de Caritat, and John Wilford
Earth Syst. Sci. Data, 15, 2465–2482, https://doi.org/10.5194/essd-15-2465-2023, https://doi.org/10.5194/essd-15-2465-2023, 2023
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With a higher demand for lithium (Li), a better understanding of its concentration and spatial distribution is important to delineate potential anomalous areas. This study uses a framework that combines data from recent geochemical surveys and relevant environmental factors to predict and map Li content across Australia. The map shows high Li concentration around existing mines and other potentially anomalous Li areas. The same mapping principles can potentially be applied to other elements.
Danilo César de Mello, Clara Glória Oliveira Baldi, Cássio Marques Moquedace, Isabelle de Angeli Oliveira, Gustavo Vieira Veloso, Lucas Carvalho Gomes, Márcio Rocha Francelino, Carlos Ernesto Gonçalves Reynaud Schaefer, Elpídio Inácio Fernandes-Filho, Edgar Batista de Medeiros Júnior, Fabio Soares de Oliveira, José João Lelis Leal de Souza Souza, Tiago Ferreira, and José A. M. Demattê
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The study explores Maritime Antarctica's geology, shaped by periglacial forces, using pioneering gamma-spectrometric and magnetic surveys on igneous rocks due to limited Antarctic surveys. Machine learning predicts radionuclide and magnetic content based on terrain features, linking their distribution to landscape processes, morphometrics, lithology, and pedogeomorphology. Inaccuracies arise due to complex periglacial processes and landscape complexities.
Frisa Irawan Ginting, Rudiyanto Rudiyanto, Fatchurahman, Ramisah Mohd Shah, Norhidayah Che Soh, Sunny Goh Eng Giap, Dian Fiantis, Budi Indra Setiawan, Sam Schiller, Aaron Davitt, and Budiman Minasny
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This study is the first to map rice cropping intensity and the harvested area across Southeast Asia at a spatial resolution of 10 m (SEA-Rice-Ci10). We have developed a geospatial inventory of paddy rice parcels and rice cropping intensity by integrating Sentinel-1 and 2 time-series data in a framework called LUCK-PALM, based on local phenological expert interpretation. According to our best knowledge, it is the finest-resolution and most accurate database of paddy rice in Southeast Asia.
Tobias Karl David Weber, Lutz Weihermüller, Attila Nemes, Michel Bechtold, Aurore Degré, Efstathios Diamantopoulos, Simone Fatichi, Vilim Filipović, Surya Gupta, Tobias L. Hohenbrink, Daniel R. Hirmas, Conrad Jackisch, Quirijn de Jong van Lier, John Koestel, Peter Lehmann, Toby R. Marthews, Budiman Minasny, Holger Pagel, Martine van der Ploeg, Simon Fiil Svane, Brigitta Szabó, Harry Vereecken, Anne Verhoef, Michael Young, Yijian Zeng, Yonggen Zhang, and Sara Bonetti
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Pedotransfer functions (PTFs) are used to predicts parameters of models describing the hydraulic properties of soils. The appropriateness of these predictions critically rely on the nature of the datasets for training the PTFs as well the physical comprehensiveness of the models. This roadmap papers is addressed at PTF developers and users, and critically reflects the utility and future of PTFs. To this end, we present a manifesto aiming at a paradigm shift in PTFs research.
Wartini Ng, Budiman Minasny, Alex McBratney, Patrice de Caritat, and John Wilford
Earth Syst. Sci. Data, 15, 2465–2482, https://doi.org/10.5194/essd-15-2465-2023, https://doi.org/10.5194/essd-15-2465-2023, 2023
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With a higher demand for lithium (Li), a better understanding of its concentration and spatial distribution is important to delineate potential anomalous areas. This study uses a framework that combines data from recent geochemical surveys and relevant environmental factors to predict and map Li content across Australia. The map shows high Li concentration around existing mines and other potentially anomalous Li areas. The same mapping principles can potentially be applied to other elements.
Mercedes Román Dobarco, Alexandre M. J-C. Wadoux, Brendan Malone, Budiman Minasny, Alex B. McBratney, and Ross Searle
Biogeosciences, 20, 1559–1586, https://doi.org/10.5194/bg-20-1559-2023, https://doi.org/10.5194/bg-20-1559-2023, 2023
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Soil organic carbon (SOC) is of a heterogeneous nature and varies in chemistry, stabilisation mechanisms, and persistence in soil. In this study we mapped the stocks of SOC fractions with different characteristics and turnover rates (presumably PyOC >= MAOC > POC) across Australia, combining spectroscopy and digital soil mapping. The SOC stocks (0–30 cm) were estimated as 13 Pg MAOC, 2 Pg POC, and 5 Pg PyOC.
Danilo César de Mello, Tiago Osório Ferreira, Gustavo Vieira Veloso, Marcos Guedes de Lana, Fellipe Alcantara de Oliveira Mello, Luis Augusto Di Loreto Di Raimo, Diego Ribeiro Oquendo Cabrero, José João Lelis Leal de Souza, Elpídio Inácio Fernandes-Filho, Márcio Rocha Francelino, Carlos Ernesto Gonçalves Reynaud Schaefer, and José A. M. Demattê
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We proposed a different method to evaluate different intensities of weathering in a heterogeneous area (soils, geology and relief) and small number of samples. We use combined data from three geophysical sensors, clustering and machine learning (nested-leave-one-out-cross-validation) to distinguish weathering intensities and assess the relationship of these variables with weathering, relief, geology, and soil types and attributes. and we obtained satisfactory performances of models evaluation.
Danilo César de Mello, Gustavo Vieira Veloso, Marcos Guedes de Lana, Fellipe Alcantara de Oliveira Mello, Raul Roberto Poppiel, Diego Ribeiro Oquendo Cabrero, Luis Augusto Di Loreto Di Raimo, Carlos Ernesto Gonçalves Reynaud Schaefer, Elpídio Inácio Fernandes Filho, Emilson Pereira Leite, and José Alexandre Melo Demattê
Geosci. Model Dev., 15, 1219–1246, https://doi.org/10.5194/gmd-15-1219-2022, https://doi.org/10.5194/gmd-15-1219-2022, 2022
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We used soil parent material, terrain attributes, and geophysical data from the soil surface to test and compare different and unprecedented geophysical sensor combination, as well as different machine learning algorithms to model and predict several soil attributes. Also, we analyzed the importance of pedoenvironmental variables. The soil attributes were modeled throughout different machine learning algorithms and related to different geophysical sensor combinations.
José Padarian, Budiman Minasny, Alex B. McBratney, and Pete Smith
SOIL Discuss., https://doi.org/10.5194/soil-2021-73, https://doi.org/10.5194/soil-2021-73, 2021
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Soil organic carbon sequestration is considered an attractive technology to partially mitigate climate change. Here, we show how the SOC storage potential varies globally. The estimated additional SOC storage potential in the topsoil of global croplands (29–67 Pg C) equates to only 2 to 5 years of emissions offsetting and 32 % of agriculture's 92 Pg historical carbon debt. Since SOC is temperature-dependent, this potential is likely to reduce by 18 % by 2040 due to climate change.
José Padarian, Alex B. McBratney, and Budiman Minasny
SOIL, 6, 389–397, https://doi.org/10.5194/soil-6-389-2020, https://doi.org/10.5194/soil-6-389-2020, 2020
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In this paper we introduce the use of game theory to interpret a digital soil mapping (DSM) model to understand the contribution of environmental factors to the prediction of soil organic carbon (SOC) in Chile. The analysis corroborated that the SOC model is capturing sensible relationships between SOC and climatic and topographical factors. We were able to represent them spatially (map) addressing the limitations of the current interpretation of models in DSM.
Yosra Ellili-Bargaoui, Brendan Philip Malone, Didier Michot, Budiman Minasny, Sébastien Vincent, Christian Walter, and Blandine Lemercier
SOIL, 6, 371–388, https://doi.org/10.5194/soil-6-371-2020, https://doi.org/10.5194/soil-6-371-2020, 2020
Sanjeewani Nimalka Somarathna Pallegedara Dewage, Budiman Minasny, and Brendan Malone
SOIL, 6, 359–369, https://doi.org/10.5194/soil-6-359-2020, https://doi.org/10.5194/soil-6-359-2020, 2020
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Most soil management activities are implemented at farm scale, yet digital soil maps are commonly available at regional/national scales. This study proposes Bayesian area-to-point kriging to downscale regional-/national-scale soil property maps to farm scale. A regional soil carbon map with a resolution of 100 m (block support) was disaggregated to 10 m (point support) information for a farm in northern NSW, Australia. Results are presented with the uncertainty of the downscaling process.
Andre Carnieletto Dotto, Jose A. M. Demattê, Raphael A. Viscarra Rossel, and Rodnei Rizzo
SOIL, 6, 163–177, https://doi.org/10.5194/soil-6-163-2020, https://doi.org/10.5194/soil-6-163-2020, 2020
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The objective of this study was to develop a soil grouping system based on spectral, climate, and terrain variables with the aim of developing a quantitative way to classify soils. To derive the new system, we applied the above-mentioned variables using cluster analysis and defined eight groups or "soil environment groupings" (SEGs). The SEG system facilitated the identification of groups with similar characteristics using not only soil but also environmental variables for their distinction.
José Padarian, Budiman Minasny, and Alex B. McBratney
SOIL, 6, 35–52, https://doi.org/10.5194/soil-6-35-2020, https://doi.org/10.5194/soil-6-35-2020, 2020
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The application of machine learning (ML) has shown an accelerated adoption in soil sciences. It is a difficult task to manually review all papers on the application of ML. This paper aims to provide a review of the application of ML aided by topic modelling in order to find patterns in a large collection of publications. The objective is to gain insight into the applications and to discuss research gaps. We found 12 main topics and that ML methods usually perform better than traditional ones.
Alexandre M. J.-C. Wadoux, José Padarian, and Budiman Minasny
SOIL, 5, 107–119, https://doi.org/10.5194/soil-5-107-2019, https://doi.org/10.5194/soil-5-107-2019, 2019
José Padarian, Budiman Minasny, and Alex B. McBratney
SOIL, 5, 79–89, https://doi.org/10.5194/soil-5-79-2019, https://doi.org/10.5194/soil-5-79-2019, 2019
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Digital soil mapping has been widely used as a cost-effective method for generating soil maps. DSM models are usually calibrated using point observations and rarely incorporate contextual information of the landscape. Here, we use convolutional neural networks to incorporate spatial context. We used as input a 3-D stack of covariate images to simultaneously predict organic carbon content at multiple depths. In this study, our model reduced the error by 30 % compared with conventional techniques.
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Soil amendment with artificial black carbon (BC; biomass transformed by incomplete combustion) has the potential to mitigate climate change. Nevertheless, the accurate quantification of BC in soil remains a critical issue. Here, we successfully used dynamic thermal analysis (DTA) to quantify centennial BC in soil. We demonstrate that DTA is largely under-exploited despite providing rapid and low-cost quantitative information over the range of soil organic matter.
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SOIL, 8, 223–235, https://doi.org/10.5194/soil-8-223-2022, https://doi.org/10.5194/soil-8-223-2022, 2022
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Elad Levintal, Yonatan Ganot, Gail Taylor, Peter Freer-Smith, Kosana Suvocarev, and Helen E. Dahlke
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SOIL, 7, 717–731, https://doi.org/10.5194/soil-7-717-2021, https://doi.org/10.5194/soil-7-717-2021, 2021
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This work delivers openly accessible and validated calibrations for diagnosing 26 soil properties based on mid-infrared spectroscopy. These were developed for four regions in Burkina Faso and Côte d'Ivoire, including 80 fields of smallholder farmers. The models can help to site-specifically and cost-efficiently monitor soil quality and fertility constraints to ameliorate soils and yields of yam or other staple crops in the four regions between the humid forest and the northern Guinean savanna.
Laura Summerauer, Philipp Baumann, Leonardo Ramirez-Lopez, Matti Barthel, Marijn Bauters, Benjamin Bukombe, Mario Reichenbach, Pascal Boeckx, Elizabeth Kearsley, Kristof Van Oost, Bernard Vanlauwe, Dieudonné Chiragaga, Aimé Bisimwa Heri-Kazi, Pieter Moonen, Andrew Sila, Keith Shepherd, Basile Bazirake Mujinya, Eric Van Ranst, Geert Baert, Sebastian Doetterl, and Johan Six
SOIL, 7, 693–715, https://doi.org/10.5194/soil-7-693-2021, https://doi.org/10.5194/soil-7-693-2021, 2021
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We present a soil mid-infrared library with over 1800 samples from central Africa in order to facilitate soil analyses of this highly understudied yet critical area. Together with an existing continental library, we demonstrate a regional analysis and geographical extrapolation to predict total carbon and nitrogen. Our results show accurate predictions and highlight the value that the data contribute to existing libraries. Our library is openly available for public use and for expansion.
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SOIL, 7, 525–546, https://doi.org/10.5194/soil-7-525-2021, https://doi.org/10.5194/soil-7-525-2021, 2021
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Kpade O. L. Hounkpatin, Johan Stendahl, Mattias Lundblad, and Erik Karltun
SOIL, 7, 377–398, https://doi.org/10.5194/soil-7-377-2021, https://doi.org/10.5194/soil-7-377-2021, 2021
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Forests store large amounts of carbon in soils. Implementing suitable measures to improve the sink potential of forest soils would require accurate data on the carbon stored in forest soils and a better understanding of the factors affecting this storage. This study showed that the prediction of soil carbon stock in Swedish forest soils can increase in accuracy when one divides a big region into smaller areas in combination with information collected locally and derived from satellites.
Hana Beitlerová, Jonas Lenz, Jan Devátý, Martin Mistr, Jiří Kapička, Arno Buchholz, Ilona Gerndtová, and Anne Routschek
SOIL, 7, 241–253, https://doi.org/10.5194/soil-7-241-2021, https://doi.org/10.5194/soil-7-241-2021, 2021
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This study presents transfer functions for a calibration parameter of the Green–Ampt infiltration module of the EROSION-2D/3D model, which are significantly improving the model performance compared to the current state. The relationships found between calibration parameters and soil parameters however put the Green–Ampt implementation in the model and the state-of-the-art parametrization method in question. A new direction of the infiltration module development is proposed.
Anatol Helfenstein, Philipp Baumann, Raphael Viscarra Rossel, Andreas Gubler, Stefan Oechslin, and Johan Six
SOIL, 7, 193–215, https://doi.org/10.5194/soil-7-193-2021, https://doi.org/10.5194/soil-7-193-2021, 2021
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In this study, we show that a soil spectral library (SSL) can be used to predict soil carbon at new and very different locations. The importance of this finding is that it requires less time-consuming lab work than calibrating a new model for every local application, while still remaining similar to or more accurate than local models. Furthermore, we show that this method even works for predicting (drained) peat soils, using a SSL with mostly mineral soils containing much less soil carbon.
Jennifer M. Rhymes, Irene Cordero, Mathilde Chomel, Jocelyn M. Lavallee, Angela L. Straathof, Deborah Ashworth, Holly Langridge, Marina Semchenko, Franciska T. de Vries, David Johnson, and Richard D. Bardgett
SOIL, 7, 95–106, https://doi.org/10.5194/soil-7-95-2021, https://doi.org/10.5194/soil-7-95-2021, 2021
Matthew A. Belanger, Carmella Vizza, G. Philip Robertson, and Sarah S. Roley
SOIL, 7, 47–52, https://doi.org/10.5194/soil-7-47-2021, https://doi.org/10.5194/soil-7-47-2021, 2021
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Soil health is often assessed by re-wetting a dry soil and measuring CO2 production, but the potential bias introduced by soils of different moisture contents is unclear. Our study found that wetter soil tended to lose more carbon during drying than drier soil, thus affecting soil health interpretations. We developed a correction factor to account for initial soil moisture effects, which future studies may benefit from adapting for their soil.
José Padarian, Alex B. McBratney, and Budiman Minasny
SOIL, 6, 389–397, https://doi.org/10.5194/soil-6-389-2020, https://doi.org/10.5194/soil-6-389-2020, 2020
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In this paper we introduce the use of game theory to interpret a digital soil mapping (DSM) model to understand the contribution of environmental factors to the prediction of soil organic carbon (SOC) in Chile. The analysis corroborated that the SOC model is capturing sensible relationships between SOC and climatic and topographical factors. We were able to represent them spatially (map) addressing the limitations of the current interpretation of models in DSM.
Yosra Ellili-Bargaoui, Brendan Philip Malone, Didier Michot, Budiman Minasny, Sébastien Vincent, Christian Walter, and Blandine Lemercier
SOIL, 6, 371–388, https://doi.org/10.5194/soil-6-371-2020, https://doi.org/10.5194/soil-6-371-2020, 2020
Anders Bjørn Møller, Amélie Marie Beucher, Nastaran Pouladi, and Mogens Humlekrog Greve
SOIL, 6, 269–289, https://doi.org/10.5194/soil-6-269-2020, https://doi.org/10.5194/soil-6-269-2020, 2020
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Decision trees have become a widely adapted tool for mapping soil properties in geographic space. However, it is problematic to implement spatial relationships in the models. We present a new method which uses geographic coordinates along several axes tilted at oblique angles in the models. We test this method on four spatial datasets. The results show that the new method is at least as accurate as other proposed alternatives, has a computational advantage and is flexible and interpretable.
Anika Gebauer, Monja Ellinger, Victor M. Brito Gomez, and Mareike Ließ
SOIL, 6, 215–229, https://doi.org/10.5194/soil-6-215-2020, https://doi.org/10.5194/soil-6-215-2020, 2020
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Pedotransfer functions (PTFs) for soil water retention were developed for two tropical soil landscapes using machine learning. The models corresponding to these PTFs had to be adjusted by tuning their parameters. The standard tuning approach was compared to mathematical optimization. The latter resulted in much better model performance. The PTFs derived are of particular importance for soil process and hydrological models.
Dominika Lewicka-Szczebak and Reinhard Well
SOIL, 6, 145–152, https://doi.org/10.5194/soil-6-145-2020, https://doi.org/10.5194/soil-6-145-2020, 2020
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This study aimed at comparison of various experimental strategies for incubating soil samples to determine the N2 flux. Such experiments require addition of isotope tracer, i.e. nitrogen fertilizer enriched in heavy nitrogen isotopes (15N). Here we compared the impact of soil homogenization and mixing with the tracer and tracer injection to the intact soil cores. The results are well comparable: both techniques would provide similar conclusions on the magnitude of N2 flux.
José Padarian and Alex B. McBratney
SOIL, 6, 89–94, https://doi.org/10.5194/soil-6-89-2020, https://doi.org/10.5194/soil-6-89-2020, 2020
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Data sharing and collaboration are critical to solving large-scale problems. The prevailing soil data-sharing model is of a centralized nature and, consequently, results in the participants ceding control and governance over their data to the lead party. Here we explore the use of a distributed ledger (blockchain) to solve the aforementioned issues. We also describe the potential use case of developing a global soil spectral library between multiple, international institutions.
José Padarian, Budiman Minasny, and Alex B. McBratney
SOIL, 6, 35–52, https://doi.org/10.5194/soil-6-35-2020, https://doi.org/10.5194/soil-6-35-2020, 2020
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The application of machine learning (ML) has shown an accelerated adoption in soil sciences. It is a difficult task to manually review all papers on the application of ML. This paper aims to provide a review of the application of ML aided by topic modelling in order to find patterns in a large collection of publications. The objective is to gain insight into the applications and to discuss research gaps. We found 12 main topics and that ML methods usually perform better than traditional ones.
Sören Thiele-Bruhn, Michael Schloter, Berndt-Michael Wilke, Lee A. Beaudette, Fabrice Martin-Laurent, Nathalie Cheviron, Christian Mougin, and Jörg Römbke
SOIL, 6, 17–34, https://doi.org/10.5194/soil-6-17-2020, https://doi.org/10.5194/soil-6-17-2020, 2020
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Soil quality depends on the functioning of soil microbiota. Only a few standardized methods are available to assess this as well as adverse effects of human activities. So we need to identify promising additional methods that target soil microbial function. Discussed are (i) molecular methods using qPCR for new endpoints, e.g. in N and P cycling and greenhouse gas emissions, (ii) techniques for fungal enzyme activities, and (iii) field methods on carbon turnover such as the litter bag test.
Jeroen H. T. Zethof, Martin Leue, Cordula Vogel, Shane W. Stoner, and Karsten Kalbitz
SOIL, 5, 383–398, https://doi.org/10.5194/soil-5-383-2019, https://doi.org/10.5194/soil-5-383-2019, 2019
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A widely overlooked source of carbon (C) in the soil environment is organic C of geogenic origin, e.g. graphite. Appropriate methods are not available to quantify graphite and to differentiate it from other organic and inorganic C sources in soils. Therefore, we examined Fourier transform infrared spectroscopy, thermogravimetric analysis and the smart combustion method for their ability to identify and quantify graphitic C in soils. The smart combustion method showed the most promising results.
Monja Ellinger, Ines Merbach, Ulrike Werban, and Mareike Ließ
SOIL, 5, 275–288, https://doi.org/10.5194/soil-5-275-2019, https://doi.org/10.5194/soil-5-275-2019, 2019
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Vis–NIR spectrometry is often applied to capture soil organic carbon (SOC). This study addresses the impact of the involved data and modelling aspects on SOC precision with a focus on the propagation of input data uncertainties. It emphasizes the necessity of transparent documentation of the measurement protocol and the model building and validation procedure. Particularly, when Vis–NIR spectrometry is used for soil monitoring, the aspect of uncertainty propagation becomes essential.
José Padarian and Ignacio Fuentes
SOIL, 5, 177–187, https://doi.org/10.5194/soil-5-177-2019, https://doi.org/10.5194/soil-5-177-2019, 2019
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A large amount of descriptive information is available in geosciences. Considering the advances in natural language it is possible to
rescuethis information and transform it into a numerical form (embeddings). We used 280764 full-text scientific articles to train a language model capable of generating such embeddings. Our domain-specific embeddings (GeoVec) outperformed general domain embedding tasks such as analogies, relatedness, and categorisation, and can be used in novel applications.
Cathelijne R. Stoof, Jasper H. J. Candel, Laszlo A. G. M. van der Wal, and Gert Peek
SOIL, 5, 159–175, https://doi.org/10.5194/soil-5-159-2019, https://doi.org/10.5194/soil-5-159-2019, 2019
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Teaching and outreach of soils is often done with real-life snapshots of soils and sediments in lacquer or glue peels. While it may seem hard, anyone can make such a peel. Illustrated with handmade drawings and an instructional video, we explain how to capture soils in peels using readily available materials. A new twist to old methods makes this safer, simpler, and more successful, and thus a true DIY (do-it-yourself) activity, highlighting the value and beauty of the ground below our feet.
Alexandre M. J.-C. Wadoux, José Padarian, and Budiman Minasny
SOIL, 5, 107–119, https://doi.org/10.5194/soil-5-107-2019, https://doi.org/10.5194/soil-5-107-2019, 2019
José Padarian, Budiman Minasny, and Alex B. McBratney
SOIL, 5, 79–89, https://doi.org/10.5194/soil-5-79-2019, https://doi.org/10.5194/soil-5-79-2019, 2019
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Digital soil mapping has been widely used as a cost-effective method for generating soil maps. DSM models are usually calibrated using point observations and rarely incorporate contextual information of the landscape. Here, we use convolutional neural networks to incorporate spatial context. We used as input a 3-D stack of covariate images to simultaneously predict organic carbon content at multiple depths. In this study, our model reduced the error by 30 % compared with conventional techniques.
Mario Guevara, Guillermo Federico Olmedo, Emma Stell, Yusuf Yigini, Yameli Aguilar Duarte, Carlos Arellano Hernández, Gloria E. Arévalo, Carlos Eduardo Arroyo-Cruz, Adriana Bolivar, Sally Bunning, Nelson Bustamante Cañas, Carlos Omar Cruz-Gaistardo, Fabian Davila, Martin Dell Acqua, Arnulfo Encina, Hernán Figueredo Tacona, Fernando Fontes, José Antonio Hernández Herrera, Alejandro Roberto Ibelles Navarro, Veronica Loayza, Alexandra M. Manueles, Fernando Mendoza Jara, Carolina Olivera, Rodrigo Osorio Hermosilla, Gonzalo Pereira, Pablo Prieto, Iván Alexis Ramos, Juan Carlos Rey Brina, Rafael Rivera, Javier Rodríguez-Rodríguez, Ronald Roopnarine, Albán Rosales Ibarra, Kenset Amaury Rosales Riveiro, Guillermo Andrés Schulz, Adrian Spence, Gustavo M. Vasques, Ronald R. Vargas, and Rodrigo Vargas
SOIL, 4, 173–193, https://doi.org/10.5194/soil-4-173-2018, https://doi.org/10.5194/soil-4-173-2018, 2018
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We provide a reproducible multi-modeling approach for SOC mapping across Latin America on a country-specific basis as required by the Global Soil Partnership of the United Nations. We identify key prediction factors for SOC across each country. We compare and test different methods to generate spatially explicit predictions of SOC and conclude that there is no best method on a quantifiable basis.
Louis-Pierre Comeau, Derrick Y. F. Lai, Jane Jinglan Cui, and Jenny Farmer
SOIL, 4, 141–152, https://doi.org/10.5194/soil-4-141-2018, https://doi.org/10.5194/soil-4-141-2018, 2018
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To date, there are still many uncertainties and unknowns regarding the soil respiration partitioning procedures. This study compared the suitability and accuracy of five different respiration partitioning methods. A qualitative evaluation table of the partition methods with five performance parameters was produced. Overall, no systematically superior or inferior partition method was found and the combination of two or more methods optimizes assessment reliability.
Jacqueline R. England and Raphael A. Viscarra Rossel
SOIL, 4, 101–122, https://doi.org/10.5194/soil-4-101-2018, https://doi.org/10.5194/soil-4-101-2018, 2018
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Proximal sensing can be used for soil C accounting, but the methods need to be standardized and procedural guidelines developed to ensure proficient measurement and accurate reporting. This is particularly important if there are financial incentives for landholders to adopt practices to sequester C. We review sensing for C accounting and discuss the requirements for the development of new soil C accounting methods based on sensing, including requirements for reporting, auditing and verification.
Madlene Nussbaum, Kay Spiess, Andri Baltensweiler, Urs Grob, Armin Keller, Lucie Greiner, Michael E. Schaepman, and Andreas Papritz
SOIL, 4, 1–22, https://doi.org/10.5194/soil-4-1-2018, https://doi.org/10.5194/soil-4-1-2018, 2018
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This paper presents an extensive evaluation of digital soil mapping (DSM) tools. Recently, large sets of environmental covariates (e.g. from analysis of terrain on multiple scales) have become more common for DSM. Many DSM studies, however, only compared DSM methods using less than 30 covariates or tested approaches on few responses. We built DSM models from 300–500 covariates using six approaches that are either popular in DSM or promising for large covariate sets.
R. Murray Lark, Elliott M. Hamilton, Belinda Kaninga, Kakoma K. Maseka, Moola Mutondo, Godfrey M. Sakala, and Michael J. Watts
SOIL, 3, 235–244, https://doi.org/10.5194/soil-3-235-2017, https://doi.org/10.5194/soil-3-235-2017, 2017
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An advantage of geostatistics for mapping soil properties is that, given a statistical model of the variable of interest, we can make a rational decision about how densely to sample so that the map is sufficiently precise. However, uncertainty about the statistical model affects this process. In this paper we show how Bayesian methods can be used to support decision making on sampling with an uncertain model, ensuring that the probability of meeting certain levels of precision is high enough.
Madlene Nussbaum, Lorenz Walthert, Marielle Fraefel, Lucie Greiner, and Andreas Papritz
SOIL, 3, 191–210, https://doi.org/10.5194/soil-3-191-2017, https://doi.org/10.5194/soil-3-191-2017, 2017
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Digital soil mapping (DSM) relates soil property data to environmental data that describe soil-forming factors. With imagery sampled from satellites or terrain analysed at multiple scales, large sets of possible input to DSM are available. We propose a new statistical framework (geoGAM) that selects parsimonious models for DSM and illustrate the application of geoGAM to two study regions. Straightforward interpretation of the modelled effects likely improves end-user acceptance of DSM products.
Hannes Keck, Bjarne W. Strobel, Jon Petter Gustafsson, and John Koestel
SOIL, 3, 177–189, https://doi.org/10.5194/soil-3-177-2017, https://doi.org/10.5194/soil-3-177-2017, 2017
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Several studies have shown that the cation adsorption sites in soils are heterogeneously distributed in space. In many soil system models this knowledge is not included yet. In our study we proposed a new method to map the 3-D distribution of cation adsorption sites in undisturbed soils. The method is based on three-dimensional X-ray scanning with a contrast agent and image analysis. We are convinced that this approach will strongly aid the development of more realistic soil system models.
Laura Arata, Katrin Meusburger, Alexandra Bürge, Markus Zehringer, Michael E. Ketterer, Lionel Mabit, and Christine Alewell
SOIL, 3, 113–122, https://doi.org/10.5194/soil-3-113-2017, https://doi.org/10.5194/soil-3-113-2017, 2017
Christopher Poeplau, Cora Vos, and Axel Don
SOIL, 3, 61–66, https://doi.org/10.5194/soil-3-61-2017, https://doi.org/10.5194/soil-3-61-2017, 2017
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This paper shows that three out of four frequently used methods to calculate soil organic carbon stocks lead to systematic overestimation of those stocks. Stones, which can be assumed to be free of carbon, have to be corrected for in both bulk density and layer thickness. We used data of the German Agricultural Soil Inventory to illustrate the potential bias and suggest a unified and unbiased calculation method for stocks of soil organic carbon, which is the largest terrestrial carbon pool.
Jan M. van Mourik, Thomas V. Wagner, J. Geert de Boer, and Boris Jansen
SOIL, 2, 299–310, https://doi.org/10.5194/soil-2-299-2016, https://doi.org/10.5194/soil-2-299-2016, 2016
Ranjith P. Udawatta, Clark J. Gantzer, Stephen H. Anderson, and Shmuel Assouline
SOIL, 2, 211–220, https://doi.org/10.5194/soil-2-211-2016, https://doi.org/10.5194/soil-2-211-2016, 2016
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Soil compaction degrades soil structure and affects water, heat, and gas exchange as well as root penetration and crop production. The objective of this study was to use X-ray computed microtomography (CMT) techniques to compare differences in geometrical soil pore parameters as influenced by compaction of two different aggregate size classes.
B. Reidy, I. Simo, P. Sills, and R. E. Creamer
SOIL, 2, 25–39, https://doi.org/10.5194/soil-2-25-2016, https://doi.org/10.5194/soil-2-25-2016, 2016
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This study reviews pedotransfer functions from the literature for different soil and horizon types. It uses these formulae to predict bulk density (ρb) per horizon using measured data of other soil properties. These data were compared to known pb per horizon and recalibrated. These calculations were used to fill missing horizon data in the Irish soil database. This allowed the generation of a pb map to 50 cm. These pb data are at horizon level allowing more accurate estimation of C with depth.
J. J. Keizer, M. A. S. Martins, S. A. Prats, L. F. Santos, D. C. S. Vieira, R. Nogueira, and L. Bilro
SOIL, 1, 641–650, https://doi.org/10.5194/soil-1-641-2015, https://doi.org/10.5194/soil-1-641-2015, 2015
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In this study, a novel plastic optical fibre turbidity sensor was exhaustively tested with a large set of runoff samples, mainly from a recently burnt area. The different types of samples from the distinct study sites revealed without exception an increase in normalized light loss with increasing sediment concentrations that agreed (reasonably) well with a power function. Nevertheless, sensor-based predictions of sediment concentration should ideally involve site-specific calibrations.
C. Rasmussen, R. E. Gallery, and J. S. Fehmi
SOIL, 1, 631–639, https://doi.org/10.5194/soil-1-631-2015, https://doi.org/10.5194/soil-1-631-2015, 2015
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There is a need to understand the response of soil systems to predicted climate warming for modeling soil processes. Current experimental methods for soil warming include expensive and difficult to implement active and passive techniques. Here we test a simple, inexpensive in situ passive soil heating approach, based on easy to construct infrared mirrors that do not require automation or enclosures. Results indicated that the infrared mirrors yielded significant heating and drying of soils.
E. Nadal-Romero, J. Revuelto, P. Errea, and J. I. López-Moreno
SOIL, 1, 561–573, https://doi.org/10.5194/soil-1-561-2015, https://doi.org/10.5194/soil-1-561-2015, 2015
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Geomatic techniques have been routinely applied in erosion studies, providing the opportunity to build high-resolution topographic models.The aim of this study is to assess and compare the functioning of terrestrial laser scanner and close range photogrammetry techniques to evaluate erosion and deposition processes in a humid badlands area.
Our results demonstrated that north slopes experienced more intense and faster dynamics than south slopes as well as the highest erosion rates.
L. M. Thomsen, J. E. M. Baartman, R. J. Barneveld, T. Starkloff, and J. Stolte
SOIL, 1, 399–410, https://doi.org/10.5194/soil-1-399-2015, https://doi.org/10.5194/soil-1-399-2015, 2015
B. A. Miller, S. Koszinski, M. Wehrhan, and M. Sommer
SOIL, 1, 217–233, https://doi.org/10.5194/soil-1-217-2015, https://doi.org/10.5194/soil-1-217-2015, 2015
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There are many different strategies for mapping SOC, among which is to model the variables needed to calculate the SOC stock indirectly or to model the SOC stock directly. The purpose of this research was to compare these two approaches for mapping SOC stocks from multiple linear regression models applied at the landscape scale via spatial association. Although the indirect approach had greater spatial variation and higher R2 values, the direct approach had a lower total estimated error.
W. Eugster and L. Merbold
SOIL, 1, 187–205, https://doi.org/10.5194/soil-1-187-2015, https://doi.org/10.5194/soil-1-187-2015, 2015
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The eddy covariance (EC) method has become increasingly popular in soil science. The basic concept of this method and its use in different types of experimental designs in the field are given, and we indicate where progress in advancing and extending the field of applications is made. The greatest strengths of EC measurements in soil science are (1) their uninterrupted continuous measurement of gas concentrations and fluxes and (2) spatial integration over
small-scale heterogeneity in the soil.
Cited articles
Acquarelli, J., van Laarhoven, T., Gerretzen, J., Tran, T. N., Buydens, L.
M. C., and Marchiori, E.: Convolutional neural networks for vibrational
spectroscopic data analysis, Anal. Chim. Acta, 954, 22–31,
https://doi.org/10.1016/j.aca.2016.12.010, 2017.
Abadi, M., Barham, P., Chen, J., Chen, Z., Davis, A., Dean, J., Devin, M., Ghemawat, S., Irving, G., Isard, M., Kudlur, M., Levenberg, J., Monga, R., Moore, S., Murray, D. G., Steiner, B., Tucker, P., Vasudevan, V., Warden, P., Wicke, M., Yu, Y., and Zheng, X.: TensorFlow: Large-scale machine learning on heterogeneous systems, Software available from tensorflow.org, available at: https://www.tensorflow.org/ (last access: 1 July 2019), 2015.
Barnes, R. J., Dhanoa, M. S., and Lister, S. J.: Standard Normal Variate
Transformation and De-Trending of near-Infrared Diffuse Reflectance Spectra,
Appl. Spectrosc., 43, 772–777, https://doi.org/10.1366/0003702894202201, 1989.
Bellinaso, H., Demattê, J. A. M., and Romeiro, S. A.: Soil Spectral
Library and Its Use in Soil Classification, Rev. Bras. Cienc. Solo, 34,
861–870, https://doi.org/10.1590/S0100-06832010000300027, 2010.
Bendor, E. and Banin, A.: Near-Infrared Analysis as a Rapid Method to
Simultaneously Evaluate Several Soil Properties, Soil Sci. Soc. Am. J., 59,
364–372, https://doi.org/10.2136/sssaj1995.03615995005900020014x, 1995.
Chang, C. W., Laird, D. A., Mausbach, M. J., and Hurburgh, C. R.:
Near-infrared reflectance spectroscopy-principal components regression
analyses of soil properties, Soil Sci. Soc. Am. J., 65, 480–490, 2001.
Chen, H. Z., Liu, Z. Y., Gu, J., Ai, W., Wen, J. B., and Cai, K.:
Quantitative analysis of soil nutrition based on FT-NIR spectroscopy
integrated with BP neural deep learning, Anal. Methods-UK, 10, 5004–5013,
https://doi.org/10.1039/c8ay01076e, 2018.
Chollet, F.: Keras, available at: https://github.com/fchollet/keras (last access: 1 July 2019), 2015.
Clark, R. N.: Chapter 1: Spectroscopy of Rocks and Minerals, and Principles
of Spectroscopy, in: Manual of Remote Sensing, edited by: Rencz, A. N.,
Remote Sensing for the Earth Sciences, John Wiley and Sons, New York, 3–58,
1999.
Cui, C. H. and Fearn, T.: Modern practical convolutional neural networks
for multivariate regression: Applications to NIR calibration, Chemometr.
Intell. Lab., 182, 9–20, https://doi.org/10.1016/j.chemolab.2018.07.008, 2018.
Dalal, R. C. and Henry, R. J.: Simultaneous Determination of Moisture,
Organic-Carbon, and Total Nitrogen by near-Infrared Reflectance
Spectrophotometry, Soil Sci. Soc. Am. J., 50, 120–123, https://doi.org/10.2136/sssaj1986.03615995005000010023x, 1986.
Dangal, S., Sanderman, J., Wills, S., and Ramirez-Lopez, L.: Accurate and
Precise Prediction of Soil Properties from a Large Mid-Infrared Spectral
Library, Soil Systems, 3, 11, https://doi.org/10.3390/soilsystems3010011, 2019.
Demattê, J. A. M.: Characterization and discrimination of soils by their
reflected electromagnetic energy, Pesqui. Agropecu. Bras., 37, 1445–1458, https://doi.org/10.1590/S0100-204x2002001000013, 2002.
Demattê, J. A. M., Bellinaso, H., Araujo, S. R., Rizzo, R., and Souza,
A. B.: Spectral regionalization of tropical soils in the estimation of soil
attributes, Rev. Cienc. Agron., 47, 589–598, 2016.
Donagema, G. K., de Campos, D. B., Calderano, S. B., Teixeira, W., and
Viana, J. M.: Manual de métodos de análise de solo, Embrapa
Solos-Documentos (INFOTECA-E), 2011.
Fang, Q., Hanlie, H., Zhao, L., Kukolich, S., Yin, K., and Wang, C.: Visible and near-infrared reflectance spectroscopy for investigating soil mineralogy, 2018, https://doi.org/10.1155/2018/3168974, 2018.
Figueroa, R. L., Zeng-Treitler, Q., Kandula, S., and Ngo, L. H.: Predicting
sample size required for classification performance, BMC Med. Inform.
Decis., 12, 8, https://doi.org/10.1186/1472-6947-12-8, 2012.
He, K. M., Zhang, X. Y., Ren, S. Q., and Sun, J.: Deep Residual Learning for
Image Recognition, 2016 Ieee Conference on Computer Vision and Pattern
Recognition (Cvpr), IEEE, 770–778, https://doi.org/10.1109/Cvpr.2016.90, 2016.
Islam, K., Singh, B., and McBratney, A.: Simultaneous estimation of several
soil properties by ultra-violet, visible, and near-infrared reflectance
spectroscopy, Aust. J. Soil Res., 41, 1101–1114, https://doi.org/10.1071/Sr02137, 2003.
Kingma, D. P. and Ba, J.: Adam: A method for stochastic optimization, arXiv
[preprint], arXiv:1412.6980, 2014.
Krizhevsky, A., Sutskever, I., and Hinton, G. E.: ImageNet classification
with deep convolutional neural networks, Proceedings of the 25th
International Conference on Neural Information Processing Systems – Volume
1, Lake Tahoe, Nevada, New York: Curran Associates, Inc., 2012.
Kuang, B. and Mouazen, A. M.: Influence of the number of samples on
prediction error of visible and near infrared spectroscopy of selected soil
properties at the farm scale, Eur. J. Soil Sci., 63, 421–429,
https://doi.org/10.1111/j.1365-2389.2012.01456.x, 2012.
Kuhn, M. and Quinlan, R.: Cubist: Rule- And Instance-Based Regression Modeling, R package version 0.2.2, available at: https://CRAN.R-project.org/package=Cubist (last access: 18 July 2019), 2018.
LeCun, Y., Bengio, Y., and Hinton, G.: Deep learning, Nature, 521, 436–444,
https://doi.org/10.1038/nature14539, 2015.
Lee, K. S., Lee, D. H., Sudduth, K. A., Chung, S. O., Kitchen, N. R., and
Drummond, S. T.: Wavelength Identification and Diffuse Reflectance
Estimation for Surface and Profile Soil Properties, T. ASABE, 52, 683–695,
2009.
Liu, L., Ji, M., and Buchroithner, M.: Transfer Learning for Soil
Spectroscopy Based on Convolutional Neural Networks and Its Application in
Soil Clay Content Mapping Using Hyperspectral Imagery, Sensors-Basel, 18, https://doi.org/10.3390/s18093169, 2018.
Mahapatra, S.: Why Deep Learning over Traditional Machine Learning?, available at: https://towardsdatascience.com/why-deep-learning-is-needed-over-traditional-machine-learning-1b6a99177063 (last access: 1 July 2019), 2018.
Mevik, B.-H., Wehrens, R., and Liland, K. H.: pls: Partial Least Squares and Principal Component Regression. R package version 2.7-0, available at: https://CRAN.R-project.org/package=pls (last access: 18 July 2019), 2018.
Ng, W., Minasny, B., Malone, B., and Filippi, P.: In search of an optimum
sampling algorithm for prediction of soil properties from infrared spectra,
PeerJ, 6, e5722, https://doi.org/10.7717/peerj.5722, 2018.
Ng, W., Minasny, B., Montazerolghaem, M., Padarian, J., Ferguson, R.,
Bailey, S., and McBratney, A. B.: Convolutional neural network for
simultaneous prediction of several soil properties using
visible/near-infrared, mid-infrared, and their combined spectra, Geoderma,
352, 251–267, https://doi.org/10.1016/j.geoderma.2019.06.016,
2019.
Padarian, J., Minasny, B., and McBratney, A. B.: Using deep learning to
predict soil properties from regional spectral data, Geoderma Regional, 16,
e00198, https://doi.org/10.1016/j.geodrs.2018.e00198, 2019.
Pinheiro, E. F. M., Ceddia, M. B., Clingensmith, C. M., Grunwald, S., and
Vasques, G. M.: Prediction of Soil Physical and Chemical Properties by
Visible and Near-Infrared Diffuse Reflectance Spectroscopy in the Central
Amazon, Remote Sens-Basel, 9, 293, https://doi.org/10.3390/rs9040293, 2017.
Python Software Foundation: Python Language Reference, Python Software Foundation, available at: https://www.python.org (last access: 1 July 2019), 2017.
Quinlan, J. R.: C4.5: Programs for Machine Learning, Morgan Kaufmann
Publishers Inc., San Mateo, California, 1993.
R Core Team: R: A language and environment for statistical computing, available at: https://www.R-project.org/ (last access: 18 July 2019), 2019.
Ramirez-Lopez, L., Schmidt, K., Behrens, T., van Wesemael, B., Dematte, J.
A. M., and Scholten, T.: Sampling optimal calibration sets in soil infrared
spectroscopy, Geoderma, 226, 140–150, https://doi.org/10.1016/j.geoderma.2014.02.002, 2014.
Rinnan, A., van den Berg, F., and Engelsen, S. B.: Review of the most common
pre-processing techniques for near-infrared spectra, Trac-Trend Anal. Chem.,
28, 1201–1222, https://doi.org/10.1016/j.trac.2009.07.007,
2009.
Savitzky, A. and Golay, M. J. E.: Smoothing and Differentiation of Data by
Simplified Least Squares Procedures, Anal. Chem., 36, 1627–1639,
https://doi.org/10.1021/ac60214a047, 1964.
Shepherd, K. D. and Walsh, M. G.: Development of Reflectance Spectral
Libraries for Characterization of Soil Properties, Soil Sci. Soc. Am. J., 66,
988–998, https://doi.org/10.2136/sssaj2002.9880, 2002.
Shibusawa, S., Imade Anom, S. W., Sato, S., Sasao, A., and Hirako, S.: Soil
mapping using the real-time soil spectrophotometer, in: ECPA, Third European Conference on Precision
Agriculture, edited by: Grenier, G. and
Blackmore, S., Agro Montpellier, 1. Montpellier, France, 497–508,
2001.
Simonyan, K. and Zisserman, A.: Very Deep Convolutional Networks for
Large-Scale Image Recognition, CoRR, abs/1409.1556, 2014.
Stenberg, B., Viscarra Rossel, R. A., Mouazen, A. M., and Wetterlind, J.:
Chapter Five – Visible and Near Infrared Spectroscopy in Soil Science, in:
Adv Agron, edited by: Sparks, D. L., Academic Press, Burlington, MA, 163–215, 2010.
Szegedy, C., Liu, W., Jia, Y. Q., Sermanet, P., Reed, S., Anguelov, D.,
Erhan, D., Vanhoucke, V., and Rabinovich, A.: Going Deeper with
Convolutions, Proc. Cvpr Ieee, Piscataway: IEEE, 1–9, 2015.
Terra, F. S., Dematte, J. A. M., and Rossel, R. A. V.: Proximal spectral
sensing in pedological assessments: vis-NIR spectra for soil classification
based on weathering and pedogenesis, Geoderma, 318, 123–136,
https://doi.org/10.1016/j.geoderma.2017.10.053, 2018.
Tsakiridis, N. L., Keramaris, K. D., Theocharis, J. B., and Zalidis, G. C.:
Simultaneous prediction of soil properties from VNIR-SWIR spectra using a
localized multi-channel 1-D convolutional neural network, Geoderma, 367,
114208, https://doi.org/10.1016/j.geoderma.2020.114208, 2020.
Viscarra Rossel, R. A. and Behrens, T.: Using data mining to model and
interpret soil diffuse reflectance spectra, Geoderma, 158, 46–54,
https://doi.org/10.1016/j.geoderma.2009.12.025, 2010.
Viscarra Rossel, R. A., Cattle, S. R., Ortega, A., and Fouad, Y.: In situ
measurements of soil colour, mineral composition and clay content by
vis–NIR spectroscopy, Geoderma, 150, 253–266, https://doi.org/10.1016/j.geoderma.2009.01.025, 2009.
Walkley, A. and Black, I. A.: An examination of the Degtjareff method for
determining soil organic matter, and a proposed modification of the chromic
acid titration method, Soil Sci., 37, 29–38, https://doi.org/10.1097/00010694-193401000-00003, 1934.
Wold, S., Martens, H., and Wold, H.: The Multivariate Calibration-Problem in
Chemistry Solved by the Pls Method, Lect. Notes Math., 973, 286–293, 1983.
Yang, J., Xu, J. F., Zhang, X. L., Wu, C. Y., Lin, T., and Ying, Y. B.: Deep
learning for vibrational spectral analysis: Recent progress and a practical
guide, Anal. Chim. Acta, 1081, 6–17, https://doi.org/10.1016/j.aca.2019.06.012, 2019.
Zhang, X. L., Xu, J. F., Yang, J., Chen, L., Zhou, H. B., Liu, X. J., Li, H.
F., Lin, T., and Ying, Y. B.: Understanding the learning mechanism of
convolutional neural networks in spectral analysis, Anal. Chim. Acta, 1119,
41–51, https://doi.org/10.1016/j.aca.2020.03.055, 2020.
Zhu, X., Vondrick, C., Fowlkes, C. C., and Ramanan, D.: Do We Need More
Training Data?, International Journal of Computer Vision, 119, 76–92,
https://doi.org/10.1007/s11263-015-0812-2, 2016.
Short summary
The number of samples utilised to create predictive models affected model performance. This research compares the number of samples needed by a deep learning model to outperform the traditional machine learning models using visible near-infrared spectroscopy data for soil properties predictions. The deep learning model was found to outperform machine learning models when the sample size was above 2000.
The number of samples utilised to create predictive models affected model performance. This...
