Merge pull request #3508 from divine7022/ic-generation

Add IC_SOILGRID_Utilities for SoilGrids Data Processing

Author: dlebauer

CHANGELOG.md

@@ -30,6 +30,10 @@ section for the next release.
 - The ERA5 NC extraction function can now handle multi-site instead of one.
 - Added function for merging images from the same tiling system (MODIS, GLANCE, ICESat-2, HLS, etc.).
 - Added function for converting images towards the GDAL-supported formats (H5, NetCDF, HDF4, GeoTIFF, etc .).
+- New utility script `IC_SOILGRID_Utilities.R` for processing SoilGrids data to generate soil carbon initial condition (IC) files. This includes  (#3508):
+  - **`soilgrids_ic_process`**: A function to extract, process, and generate ensemble members from SoilGrids250m data.
+  - **`preprocess_soilgrids_data`**: A helper function to handle missing values and ensure data integrity during preprocessing. 
+  - **`generate_soilgrids_ensemble`**: A function to create ensemble members for a site based on processed soil carbon data. 
 - `extract.nc.ERA5()` and `met2CF.ERA5` now supports both ensemble and reanalysis data processing .
 
 - Initial Quarto notebook `run_pecan.qmd` to run PEcAn Demo 1 workflow from a pre-configured `pecan.xml` file, enabling notebook-based model runs, analysis, and visualization.[#3531](https://github.com/PecanProject/pecan/pull/3531)

docker/depends/pecan_package_dependencies.csv

@@ -187,6 +187,7 @@
 "MASS","*","base/utils","Suggests",FALSE
 "MASS","*","modules/assim.batch","Imports",FALSE
 "MASS","*","modules/data.atmosphere","Imports",FALSE
+"MASS","*","modules/data.land","Suggests",FALSE
 "MASS","*","modules/meta.analysis","Imports",FALSE
 "MASS","*","modules/priors","Imports",FALSE
 "MASS","*","modules/rtm","Imports",FALSE

modules/data.land/DESCRIPTION

@@ -23,7 +23,7 @@ Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
     efficacy of scientific investigation.
 URL: https://pecanproject.github.io
 BugReports: https://github.com/PecanProject/pecan/issues
-Depends: R (>= 3.5.0)
+Depends: R (>= 4.1.0)
 Imports:
     coda,
     curl,
@@ -59,7 +59,7 @@ Imports:
     tidyr,
     tidyselect,
     traits,
-    XML (>= 3.98-1.4)      
+    XML (>= 3.98-1.4)
 Suggests:
     dataone,
     datapack,
@@ -70,7 +70,8 @@ Suggests:
     raster,
     reticulate,
     testthat (>= 1.0.2),
-    withr
+    withr,
+    MASS
 Remotes:
     github::ropensci/traits
 License: BSD_3_clause + file LICENSE

modules/data.land/NAMESPACE

@@ -28,6 +28,7 @@ export(format_identifier)
 export(from.Tag)
 export(from.TreeCode)
 export(gSSURGO.Query)
+export(generate_soilgrids_ensemble)
 export(get.attributes)
 export(get.soil)
 export(get_resource_map)
@@ -47,6 +48,7 @@ export(plot2AGB)
 export(pool_ic_list2netcdf)
 export(pool_ic_netcdf2list)
 export(prepare_pools)
+export(preprocess_soilgrids_data)
 export(put_veg_module)
 export(sample_ic)
 export(sclass)
@@ -56,6 +58,7 @@ export(soil2netcdf)
 export(soil_params)
 export(soil_params_ensemble_soilgrids)
 export(soil_process)
+export(soilgrids_ic_process)
 export(soilgrids_soilC_extract)
 export(soilgrids_texture_extraction)
 export(subset_layer)

modules/data.land/NEWS.md

@@ -1,7 +1,10 @@
 # Unreleased
 
 * Add function `clip_and_save_raster_file()` for subsetting rasters to match a polygon of interest (#3537).
-
+* New utility script `IC_SOILGRID_Utilities.R` for processing SoilGrids data to generate soil carbon initial condition (IC) files. This includes (#3508):
+  - **`soilgrids_ic_process`**: A function to extract, process, and generate ensemble members from SoilGrids250m data.
+  - **`preprocess_soilgrids_data`**: A helper function to handle missing values and ensure data integrity during preprocessing. 
+  - **`generate_soilgrids_ensemble`**: A function to create ensemble members for a site based on processed soil carbon data. 
 
 # PEcAn.data.land 1.8.2
 - Removed unused parameter `machine` from put_veg_module()
@@ -23,7 +26,7 @@
 * Included all relevant carbon pools (`ROOT_BIOMASS`, `AG_BIOMASS`, `SOIL_STOCK`, `LIT_BIOMASS`) in BADM-based IC extraction; excluded non-pool variables like `SOIL_CHEM`.
 * Added explicit support for `LIT_BIOMASS` to fully utilize **BADM** biomass capabilities.
 * Added `test-IC_BADM_Utilities.R` to validate BADM initial condition extraction and processing
-
+  
 ## Fixed
 
 * `gSSURGO.Query()` now always returns all the columns requested, even ones that are all NA. It also now always requires `mukeys` to be specified.