1. Global Soil Information Facilities
Software developments
Tomislav Hengl
ISRIC World Soil Information, Wageningen University
GSM2011.org, June 2024th 2011
2. Acknowledgement
1. Hannes Reuter GIS and WPS functionality.
2. Pierre Roudier Dylan Beaudette plotKML package.
3. Brendon Malone David Jacquier spline tting
function.
4. Keith Shepherd Bob MacMillan Soil Reference
Library.
GSM2011.org, June 2024th 2011
3. GSIF components
1. Cyber infrastructure for input, analysis and visualization of
data.
2. Global databases (legacy data, gridded covariates) that are
main inputs to global soil mapping.
3. Software tools (modules and packages) and manuals for
creation of geoinformation, for instance, according to
the GlobalSoilMap.net specications.
4. Standards and protocols for data entry, map generation and
data sharing.
GSM2011.org, June 2024th 2011
5. Overview
Open Soil Profiles Soil covariates (worldgrids)
Global Continental scale Country/state-level
Soil variables
Soil site info
Soil analytical data
Descriptive properties 5.6 km repository 1 km repository 250 m repository
R packages
Map import module
Data entry module
Harmonization module
Spline fitting
Spatial analysis module
(Servers) cyber infrastructure Data visualization
Data export
Soil property maps Webmapping API
Six+four key soil parameters
Global coverage (organic carbon, pH, clay, silt,
sand, coarse fragments)
Real-time spatial prediction
at six standard depths (0-5, 5-
(Google Maps)
15, 15-30, 30-60, 60-100, 100-
GlobalSoilMap.net functionality
200 cm)
for web-applications
and with included upper and
Geo-serving and geoprocessing
lower 95% probability ranges
functionality
100 m (250 m, 1 km and 5.6 km)
GSM2011.org, June 2024th 2011
6. GSIF modules
New soil profile
New covariates
data
MAP IMPORT MODULE DATA ENTRY MODULE
Upload of gridded maps to the soilprofiles.org: live data
soilgrids.org repository; entry forms for point data; HARMONISATION MODULE
Meta-data generation tool; Geo-registry module; Translation of laboratory
Automated map matching and Automated data screening and methods (correlation)
validation (mask maps); detection of gross errors and Upscaling / downscaling
Automated conversion and artifacts; functionality
harmonization of soil polygon Data translation (re-
maps; formatting) functionality
SPATIAL ANALYSIS MODULE
Overlay (covariates) and
regression analysis;
Multiscale prediction - trend
models;
Variogram analysis (automap);
Prediction and simulations;
Cross-validation;
Predict secondary soil
Open Soil Profiles
Soil Gridded Covariates (soilprofiles.org)
parameters (PTF)
(soilgrids.org)
DATA EXPORT MODULE SUPPORT MODULE
Subsetting and export to GIS Help and F.A.Q.
data formats (geotiff and ESRI Variable descriptions
Shape file), KML and table (meta-data)
formats (DBF); Search functionality
API services to serve the data (manuals and user
without accessing URL (e.g. forums, demos and
via mobile-phone); multimedia)
Data serving
Soil property maps
(globalsoilmap.net)
GSM2011.org, June 2024th 2011
7. Proposed implementation
1. Produce a suite of utilities to import, re-format, analyze
and visualize spatial soil data
GSM2011.org, June 2024th 2011
8. Proposed implementation
1. Produce a suite of utilities to import, re-format, analyze
and visualize spatial soil data
2. Design them so they t the needs of operational global
soil mapping
GSM2011.org, June 2024th 2011
9. Proposed implementation
1. Produce a suite of utilities to import, re-format, analyze
and visualize spatial soil data
2. Design them so they t the needs of operational global
soil mapping
3. Focus on using R+OSGeo
GSM2011.org, June 2024th 2011
10. Proposed implementation
1. Produce a suite of utilities to import, re-format, analyze
and visualize spatial soil data
2. Design them so they t the needs of operational global
soil mapping
3. Focus on using R+OSGeo
4. Get the whole DSM community involved (in design, in
development, in use)
GSM2011.org, June 2024th 2011
11. Proposed implementation
1. Produce a suite of utilities to import, re-format, analyze
and visualize spatial soil data
2. Design them so they t the needs of operational global
soil mapping
3. Focus on using R+OSGeo
4. Get the whole DSM community involved (in design, in
development, in use)
5. Provide training in development and use to countries and
nodes
GSM2011.org, June 2024th 2011
12. List of utilities
1. Global soil mapping (core) package GSIF
GSM2011.org, June 2024th 2011
13. List of utilities
1. Global soil mapping (core) package GSIF
2. Soil visualization package plotKML
GSM2011.org, June 2024th 2011
14. List of utilities
1. Global soil mapping (core) package GSIF
2. Soil visualization package plotKML
3. Soil Reference Library SRL
GSM2011.org, June 2024th 2011
15. List of utilities
1. Global soil mapping (core) package GSIF
2. Soil visualization package plotKML
3. Soil Reference Library SRL
4. Geo-services (PythonWPS, Geoserver, RServe, GDAL utilities)
GSM2011.org, June 2024th 2011
16. Functionality (GSIF)
Estimate the spatial domain and the tiling system;
Fit splines to soil horizon records and convert from block to
point support in vertical dimension;
Query and download point and gridded data from the data
portals;
Convert harmonized soil prole data from relational structure
to single table records;
Automatically lter suspicious records and detect outliers in
the soil prole records;
Generate one set of globally consistent predictions using point
observations (OSP) and gridded predictors (worldgrids);
Convert gridded predictions to formats required for submission
to GSIF;
Generate metadata and data analysis reports using XML
formats;
GSM2011.org, June 2024th 2011
17. Status (GSIF)
Progress so far:
Derive cell ID for any location in the world and estimate
number of 1degree blocks required to map an area (based on
a land mask);
Fit equal-area splines to soil prole data (the method of
Bishop et al. (1999));
Get values at point locations from worldgrids.org (covariates);
Convert site-horizon DB to single-table structure;
GSM2011.org, June 2024th 2011
18. Functionality (plotKML)
Visualize soil proles measurements (using the original soil
colors);
Visualize soil prole photographs;
Plot results of prediction (soil property maps) using standard
color schemes;
Default distribution model for the GlobalSoilMap.net property
maps (?);
Visualize uncertainty of the maps;
GSM2011.org, June 2024th 2011
29. SRL package
Harmonization of soil prole data;
Estimation of secondary soil properties using pedo-transfer
functions;
Estimation of soil properties using soil spectroscopy;
GSM2011.org, June 2024th 2011
30. Overview
SOIL REFERENCE
Soil Spectral
LIBRARY Library
Dependent R libraries Soil Reference Data
(soil referent profiles with complete Obtain additional
laboratory methods, soil description field data
soil.spec
aqp and scanned soil spectra)
soiltexture
NO
HydroMe
Conversion functions Fits
(various R packages for generalized Fit conversion requir-
linear modeling, fuzzy matching, model parameters ed accur-
regression trees etc.) acy?
YES
Design the Conversion coefficients
conversion model (most accurate models to estimate
NO standard parameters; extendible)
Convers- Estimate values of
Unharmonized Standardized value +
ion model YES the standardized
record (new data) Associated uncertainty
available? variable
GSM2011.org, June 2024th 2011
31. Status
It is not dicult to build a package, but to get soil reference
data
We would need (at least) 300500 points:
Points have to be representative (hypercube sampling, the
whole world)
Each point should be sampled using standard protocol (soil
eld description, soil lab analysis, soil spectroscopy)
Project designers need to decide if existing samples can be
used as well as new ones
We probably need new point samples
GSM2011.org, June 2024th 2011
32. ISRIC monoliths
Figure: ISRIC referent samples (monoliths) and occurrence probability.
Derived using the MaxEnt package (climatic images, HWSD and
vegetation maps).
GSM2011.org, June 2024th 2011
33. Main principles of programming
1. Hide complexity from the users (scale, eective precision, 3D
geostat)
2. Deliver data and results so that no software training is required
to open it (KML)
3. Link to R+OSGeo community (do not invent functionality that
already exists and is operational)
GSM2011.org, June 2024th 2011
34. Why R?
1. It is a trustworthy software because it is open source
GSM2011.org, June 2024th 2011
35. Why R?
1. It is a trustworthy software because it is open source
2. It is accessible to anyone via most of Operating Systems
GSM2011.org, June 2024th 2011
36. Why R?
1. It is a trustworthy software because it is open source
2. It is accessible to anyone via most of Operating Systems
3. People in developing countries can start picking things
up today!
GSM2011.org, June 2024th 2011
37. Why R?
1. It is a trustworthy software because it is open source
2. It is accessible to anyone via most of Operating Systems
3. People in developing countries can start picking things
up today!
4. It is the fastest growing open source environments for
statistical computing
GSM2011.org, June 2024th 2011
38. Why R?
1. It is a trustworthy software because it is open source
2. It is accessible to anyone via most of Operating Systems
3. People in developing countries can start picking things
up today!
4. It is the fastest growing open source environments for
statistical computing
5. It can handle space-time data
GSM2011.org, June 2024th 2011
39. Why R?
1. It is a trustworthy software because it is open source
2. It is accessible to anyone via most of Operating Systems
3. People in developing countries can start picking things
up today!
4. It is the fastest growing open source environments for
statistical computing
5. It can handle space-time data
6. It is professional (made by top-minds in the business)
GSM2011.org, June 2024th 2011
40. Next steps
Release plotKML and GSIF packages v0.1
Continue developing the functionality via R-forge
Use users feedback to improve
Optimize the processing speed and improve usability on various
platforms
Incorporate this functionality within WPS
GSM2011.org, June 2024th 2011
41. Would you like to join GSIF?
Join the GSIF workshop on Friday
GSM2011.org, June 2024th 2011
42. Would you like to join GSIF?
Join the GSIF workshop on Friday
There are some expectations:
GSM2011.org, June 2024th 2011
43. Would you like to join GSIF?
Join the GSIF workshop on Friday
There are some expectations:
1. You take a responsibility to deliver the functionality on time
GSM2011.org, June 2024th 2011
44. Would you like to join GSIF?
Join the GSIF workshop on Friday
There are some expectations:
1. You take a responsibility to deliver the functionality on time
2. You share most of the Edzer Pebesma's Open data principles
GSM2011.org, June 2024th 2011
45. Would you like to join GSIF?
Join the GSIF workshop on Friday
There are some expectations:
1. You take a responsibility to deliver the functionality on time
2. You share most of the Edzer Pebesma's Open data principles
A
3. You should be familiar with R / LTEX
GSM2011.org, June 2024th 2011
