Predictive Soil Mapping with R | Internal Links | Dofollow |
Predictive Soil Mapping for advanced R users | Internal Links | Dofollow |
Editors | Internal Links | Dofollow |
Preface | Internal Links | Dofollow |
Connected publications | Internal Links | Dofollow |
Contributions | Internal Links | Dofollow |
Reproducibility | Internal Links | Dofollow |
Acknowledgements | Internal Links | Dofollow |
1 Soil resource inventories and soil maps | Internal Links | Dofollow |
1.1 Introduction | Internal Links | Dofollow |
1.2 Soils and soil inventories | Internal Links | Dofollow |
1.2.1 Soil: a definition | Internal Links | Dofollow |
1.2.2 Soil variables | Internal Links | Dofollow |
1.2.3 Primary and secondary soil variables | Internal Links | Dofollow |
1.3 Soil mapping | Internal Links | Dofollow |
1.3.1 What are soil resource inventories? | Internal Links | Dofollow |
1.3.2 Soil mapping approaches and concepts | Internal Links | Dofollow |
1.3.3 Theoretical basis of soil mapping: in context of the universal model of spatial variation | Internal Links | Dofollow |
1.3.4 Traditional (conventional) soil mapping | Internal Links | Dofollow |
1.3.5 Variants of soil maps | Internal Links | Dofollow |
1.3.6 Predictive and automated soil mapping | Internal Links | Dofollow |
1.3.7 Comparison of conventional and pedometric or predictive soil mapping | Internal Links | Dofollow |
1.3.8 Top-down versus bottom-up approaches: subdivision versus agglomeration | Internal Links | Dofollow |
1.4 Sources of soil data for soil mapping | Internal Links | Dofollow |
1.4.1 Soil data sources targeted by PSM | Internal Links | Dofollow |
1.4.2 Field observations of soil properties | Internal Links | Dofollow |
1.4.3 Legacy soil profile data | Internal Links | Dofollow |
1.4.4 Soil covariates | Internal Links | Dofollow |
1.4.5 Soil delineations | Internal Links | Dofollow |
1.4.6 Advantages and disadvantages of using soil delineations | Internal Links | Dofollow |
1.4.7 Accuracy of conventional soil polygon maps | Internal Links | Dofollow |
1.4.8 Legacy soil expertise (tacit knowledge) | Internal Links | Dofollow |
1.4.9 Pseudo-observations | Internal Links | Dofollow |
1.5 Soil databases and soil information systems | Internal Links | Dofollow |
1.5.1 Soil databases | Internal Links | Dofollow |
1.5.2 A Soil Information System | Internal Links | Dofollow |
1.5.3 Soil information users | Internal Links | Dofollow |
1.5.4 Usability of soil geographical database | Internal Links | Dofollow |
1.6 Uncertainty of soil variables | Internal Links | Dofollow |
1.6.1 Basic concepts | Internal Links | Dofollow |
1.6.2 Sources of uncertainty | Internal Links | Dofollow |
1.6.3 Quantifying the uncertainty in soil data products | Internal Links | Dofollow |
1.6.4 Common uncertainty levels in soil maps | Internal Links | Dofollow |
1.7 Summary and conclusions | Internal Links | Dofollow |
2 Software installation and first steps | Internal Links | Dofollow |
2.1 List of software in use | Internal Links | Dofollow |
2.2 Installing software on Ubuntu OS | Internal Links | Dofollow |
2.3 Installing GIS software | Internal Links | Dofollow |
2.4 WhiteboxTools | Internal Links | Dofollow |
2.5 RStudio | Internal Links | Dofollow |
2.6 plotKML and GSIF packages | Internal Links | Dofollow |
2.7 Connecting R and SAGA GIS | Internal Links | Dofollow |
2.8 Connecting R and GDAL | Internal Links | Dofollow |
3 Soil observations and variables | Internal Links | Dofollow |
3.1 Basic concepts | Internal Links | Dofollow |
3.1.1 Types of soil observations | Internal Links | Dofollow |
3.1.2 Soil properties of interest for global soil mapping | Internal Links | Dofollow |
3.1.3 Reference methods | Internal Links | Dofollow |
3.1.4 Standard soil variables of interest for soil mapping | Internal Links | Dofollow |
3.2 Descriptive soil profile observations | Internal Links | Dofollow |
3.2.1 Depth to bedrock | Internal Links | Dofollow |
3.2.2 Effective soil depth and rooting depth | Internal Links | Dofollow |
3.3 Chemical soil properties | Internal Links | Dofollow |
3.3.1 Soil organic carbon | Internal Links | Dofollow |
3.3.2 Soil pH | Internal Links | Dofollow |
3.3.3 Soil nutrients | Internal Links | Dofollow |
3.4 Physical and hydrological soil properties | Internal Links | Dofollow |
3.4.1 Coarse fragments | Internal Links | Dofollow |
3.4.2 Particle size class distribution: sand, silt and clay | Internal Links | Dofollow |
3.4.3 Bulk density | Internal Links | Dofollow |
3.4.4 Soil organic carbon stock | Internal Links | Dofollow |
3.4.5 Available Water Capacity | Internal Links | Dofollow |
3.5 Harmonization of soil data and pedo-transfer functions | Internal Links | Dofollow |
3.5.1 Basic concepts of harmonization of soil property values | Internal Links | Dofollow |
3.5.2 Example of harmonization using texture-by-hand classes | Internal Links | Dofollow |
3.6 Soil class data | Internal Links | Dofollow |
3.6.1 Soil types | Internal Links | Dofollow |
3.6.2 Other factor-type variables | Internal Links | Dofollow |
3.7 Importing and formatting soil data in R | Internal Links | Dofollow |
3.7.1 Converting texture-by-hand classes to fractions | Internal Links | Dofollow |
3.7.2 Converting Munsell color codes to other color systems | Internal Links | Dofollow |
3.8 Using Machine Learning to build Pedo-Transfer-Functions | Internal Links | Dofollow |
3.8.1 PTF for Bulk Density | Internal Links | Dofollow |
3.8.2 PTF for correlating classification systems | Internal Links | Dofollow |
3.9 Summary points | Internal Links | Dofollow |
4 Preparation of soil covariates for soil mapping | Internal Links | Dofollow |
4.1 Soil covariate data sources | Internal Links | Dofollow |
4.1.1 Types of soil covariates | Internal Links | Dofollow |
4.1.2 Soil covariate data sources (30–100 m resolution) | Internal Links | Dofollow |
4.1.3 Soil covariate data sources (250 m resolution or coarser) | Internal Links | Dofollow |
4.2 Preparing soil covariate layers | Internal Links | Dofollow |
4.2.1 Converting polygon maps to rasters | Internal Links | Dofollow |
4.2.2 Downscaling or upscaling (aggregating) rasters | Internal Links | Dofollow |
4.2.3 Deriving DEM parameters using SAGA GIS | Internal Links | Dofollow |
4.2.4 Filtering out missing pixels and artifacts | Internal Links | Dofollow |
4.2.5 Overlaying and subsetting raster stacks and points | Internal Links | Dofollow |
4.2.6 Working with large(r) rasters | Internal Links | Dofollow |
4.3 Summary points | Internal Links | Dofollow |
5 Statistical theory for predictive soil mapping | Internal Links | Dofollow |
5.1 Aspects of spatial variability of soil variables | Internal Links | Dofollow |
5.1.1 Modelling soil variability | Internal Links | Dofollow |
5.1.2 Universal model of soil variation | Internal Links | Dofollow |
5.1.3 Modelling the variation of soil with depth | Internal Links | Dofollow |
5.1.4 Vertical aggregation of soil properties | Internal Links | Dofollow |
5.2 Spatial prediction of soil variables | Internal Links | Dofollow |
5.2.1 Main principles | Internal Links | Dofollow |
5.2.2 Soil sampling | Internal Links | Dofollow |
5.2.3 Knowledge-driven soil mapping | Internal Links | Dofollow |
5.2.4 Geostatistics-driven soil mapping (pedometric mapping) | Internal Links | Dofollow |
5.2.5 Regression-kriging (generic model) | Internal Links | Dofollow |
5.2.6 Spatial Prediction using multiple linear regression | Internal Links | Dofollow |
5.2.7 Universal kriging prediction error | Internal Links | Dofollow |
5.2.8 Regression-kriging examples | Internal Links | Dofollow |
5.2.9 Regression-kriging examples using the GSIF package | Internal Links | Dofollow |
5.2.10 Regression-kriging and polygon averaging | Internal Links | Dofollow |
5.2.11 Predictions at point vs block support | Internal Links | Dofollow |
5.2.12 Geostatistical simulations | Internal Links | Dofollow |
5.2.13 Automated mapping | Internal Links | Dofollow |
5.2.14 Selecting spatial prediction models | Internal Links | Dofollow |
5.2.15 3D regression-kriging | Internal Links | Dofollow |
5.2.16 Predicting with multiscale and multisource data | Internal Links | Dofollow |
5.3 Accuracy assessment and the mapping efficiency | Internal Links | Dofollow |
5.3.1 Mapping accuracy and numeric resolution | Internal Links | Dofollow |
5.3.2 Accuracy assessment methods | Internal Links | Dofollow |
5.3.3 Cross-validation and its limitations | Internal Links | Dofollow |
5.3.4 Accuracy of the predicted model uncertainty | Internal Links | Dofollow |
5.3.5 Derivation and interpretation of prediction interval | Internal Links | Dofollow |
5.3.6 Universal measures of mapping accuracy | Internal Links | Dofollow |
5.3.7 Mapping accuracy and soil survey costs | Internal Links | Dofollow |
5.3.8 Summary points | Internal Links | Dofollow |
6 Machine Learning Algorithms for soil mapping | Internal Links | Dofollow |
6.1 Spatial prediction of soil properties and classes using MLA’s | Internal Links | Dofollow |
6.1.1 Loading the packages and data | Internal Links | Dofollow |
6.1.2 Spatial prediction of soil classes using MLA’s | Internal Links | Dofollow |
6.1.3 Modelling numeric soil properties using h2o | Internal Links | Dofollow |
6.1.4 Spatial prediction of 3D (numeric) variables | Internal Links | Dofollow |
6.1.5 Ensemble predictions using h2oEnsemble | Internal Links | Dofollow |
6.1.6 Ensemble predictions using SuperLearner package | Internal Links | Dofollow |
6.2 A generic framework for spatial prediction using Random Forest | Internal Links | Dofollow |
6.2.1 General principle of RFsp | Internal Links | Dofollow |
6.2.2 Geographical covariates | Internal Links | Dofollow |
6.2.3 Spatial prediction 2D continuous variable using RFsp | Internal Links | Dofollow |
6.2.4 Spatial prediction 2D variable with covariates using RFsp | Internal Links | Dofollow |
6.2.5 Spatial prediction of binomial variables | Internal Links | Dofollow |
6.2.6 Spatial prediction of soil types | Internal Links | Dofollow |
6.3 Summary points | Internal Links | Dofollow |
7 Spatial prediction and assessment of Soil Organic Carbon | Internal Links | Dofollow |
7.1 Introduction | Internal Links | Dofollow |
7.2 Measurement and derivation of soil organic carbon | Internal Links | Dofollow |
7.3 Derivation of OCS and OCD using soil profile data | Internal Links | Dofollow |
7.4 Estimation of Bulk Density using a globally-calibrated PTF | Internal Links | Dofollow |
7.5 Generating maps of OCS | Internal Links | Dofollow |
7.6 Predicting OCS from point data (the 2D approach) | Internal Links | Dofollow |
7.7 Deriving OCS from soil profile data (the 3D approach) | Internal Links | Dofollow |
7.8 Deriving OCS using spatiotemporal models | Internal Links | Dofollow |
7.9 Summary points | Internal Links | Dofollow |
8 Practical tips for organizing Predictive Soil Mapping | Internal Links | Dofollow |
8.1 Critical aspects of Predictive Soil Mapping | Internal Links | Dofollow |
8.1.1 PSM main steps | Internal Links | Dofollow |
8.1.2 PSM input and output spatial data layers | Internal Links | Dofollow |
8.2 Technical specifications affecting the majority of production costs | Internal Links | Dofollow |
8.2.1 Field observations and measurements | Internal Links | Dofollow |
8.2.2 Preparation of point data | Internal Links | Dofollow |
8.2.3 Preparation of covariates | Internal Links | Dofollow |
8.2.4 Soil mask and the grid system | Internal Links | Dofollow |
8.2.5 Uncertainty of PSM maps | Internal Links | Dofollow |
8.2.6 Computing costs | Internal Links | Dofollow |
8.3 Final delivery of maps | Internal Links | Dofollow |
8.3.1 Delivery data formats | Internal Links | Dofollow |
8.3.2 General recommendations | Internal Links | Dofollow |
8.3.3 Technical specifications PSM project | Internal Links | Dofollow |
8.3.4 Standard soil data production costs | Internal Links | Dofollow |
8.4 Summary notes | Internal Links | Dofollow |
9 The future of predictive soil mapping | Internal Links | Dofollow |
9.1 Introduction | Internal Links | Dofollow |
9.2 Past conventional terrestrial resource inventories | Internal Links | Dofollow |
9.2.1 Why have most national resource inventories been discontinued? | Internal Links | Dofollow |
9.2.2 Is there a future for conventional terrestrial inventory programs? | Internal Links | Dofollow |
9.2.3 Can terrestrial inventory programs be renewed and revived? | Internal Links | Dofollow |
9.2.4 How can terrestrial inventory programs be renewed and revived and by whom? | Internal Links | Dofollow |
9.3 The future of PSM: Embracing scientific and technical advances | Internal Links | Dofollow |
9.3.1 Overview | Internal Links | Dofollow |
9.3.2 Collection of field observations and samples | Internal Links | Dofollow |
9.3.3 Collecting new field O&M data | Internal Links | Dofollow |
9.3.4 Characterization of soils in the field and the laboratory | Internal Links | Dofollow |
9.3.5 Creation, collation and distribution of effective environmental covariates | Internal Links | Dofollow |
9.3.6 Automated spatial prediction models (PSM) | Internal Links | Dofollow |
9.3.7 Hosting, publishing, sharing and using spatial data | Internal Links | Dofollow |
9.3.8 New visualization and data analysis tools | Internal Links | Dofollow |
9.4 The future of PSM: Embracing new organizational and governance models | Internal Links | Dofollow |
9.4.1 Overview | Internal Links | Dofollow |
9.4.2 Open data and platforms and procedures for acquiring and sharing it | Internal Links | Dofollow |
9.4.3 Open cloud-based processing capabilities | Internal Links | Dofollow |
9.4.4 Collaborative production of inputs and new outputs | Internal Links | Dofollow |
9.4.5 Crowdsourcing and voluntary collaboration, | Internal Links | Dofollow |
9.4.6 Sponsorship, subscription, crowdfunding and blockchain funding systems | Internal Links | Dofollow |
9.4.7 A proposal for organizing and managing a new open collective | Internal Links | Dofollow |
References | Internal Links | Dofollow |
T. (Tom) Hengl and R.A. (Bob) MacMillan | External Links | Dofollow |
Predictive Soil Mapping with R | External Links | Dofollow |
ISRIC’s | External Links | Dofollow |
github issues | External Links | Dofollow |
www.lulu.com | External Links | Dofollow |
Tom Hengl | External Links | Dofollow |
SoilGrids | External Links | Dofollow |
http://youtube.com/c/ISRICorg | External Links | Dofollow |
https://www.youtube.com/c/OpenGeoHubFoundation | External Links | Dofollow |
https://landgis.opengeohub.org | External Links | Dofollow |
Bob MacMillan | External Links | Dofollow |
http://africasoils.net | External Links | Dofollow |
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