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Landscape soil parametrization

Source: R/add_soilgrids.R
soil_parametrization.Rd

Function add_soilgrids fills column 'soil' with physical soil characteristics drawn from SoilGrids 2.0 (Hengl et al. 2017; Poggio et al. 2021). Function modify_soils modifies soil definition according to soil depth and depth to bedrock information. Function check_soils verifies that soil data does not contain missing values for key variables and, if so, assigns default values.

Usage

add_soilgrids(
  x,
  soilgrids_path = NULL,
  widths = NULL,
  replace_existing = TRUE,
  progress = TRUE
)

modify_soils(
  x,
  soil_depth_map = NULL,
  depth_to_bedrock_map = NULL,
  regolith_rfc = 97.5,
  full_rock_filling = TRUE,
  progress = TRUE
)

check_soils(
  x,
  check_equal_layers = FALSE,
  fill_missing = FALSE,
  default_values = c(clay = 25, sand = 25, bd = 1.5, rfc = 25),
  progress = FALSE
)

Arguments

x

An object of class sf with a valid CRS definition. If it contains a column called 'land_cover_type', soils will be retrieved for "agriculture" and "wildland" cover types only. Otherwise, soils are retrieved for all locations. For functions modify_soils or check_soils, x should already contain a column named "soil".

soilgrids_path

Path to SoilGrids rasters (see details). If missing, the SoilGrids REST API (https://rest.isric.org) will be queried.

widths

A numeric vector indicating the desired layer widths, in mm. If NULL the default soil grids layer definition is returned.

replace_existing

A logical flag to force the replacement of existing soil data, when already present

progress

A logical flag to include a progress bar while processing the output of the query to the SoilGrids REST API.

soil_depth_map

An object of class SpatRaster or SpatVector with the soil depth (in mm) values.

depth_to_bedrock_map

An object of class SpatRaster or SpatVector with depth to bedrock (in mm) values.

regolith_rfc

Rock fragment content, in percent volume, between soil depth and 200cm depth (or lower depths, if modified via widths).

full_rock_filling

Logical flag to modify rock fragment content in all soil layers with according to distance to soil depth.

check_equal_layers

Logical flag to test whether soils have the same number of layers.

fill_missing

Logical flag to fill missing values in key parameters with defaults.

default_values

Vector of default values for locations with missing data.

Value

A modified object of class sf with column 'soil'.

Details

If soilgrids_path = NULL the function connects with the SoilGrids REST API (https://rest.isric.org) to retrieve the soil physical and chemical characteristics for a site (Hengl et al. 2007; Poggio et al. 2021), selected by its coordinates. Also, in case the depths are not the default ones in the SoilGrids API, the function uses averages the values of soil grid layers depending on the overlap between soil layer definitions. Unfortunately, SoilGrids REST API queries are limited to a few points.

If soilgrids_path != NULL the function will read SoilGrid rasters from the file disk. Folders need to be defined for each variable ("sand", "clay", "soc", "bdod", "cfvo" and "nitrogen"). File paths from soilgrids_path should be named:

var/var_layer_mean.tif

where var is one of the above and layer is "0-5cm", "5-15cm", "15-30cm", "30-60cm", "60-100cm" or "100-200cm"

SoilGrids does not provide soil depth estimates. Function modify_soils is designed to adjust soil depths according to available information. When soil_depth_map is provided, the function adjusts rock fragment content of layers below soil depth with the value of regolith_rfc. When depth_to_bedrock_map is provided, the function truncates the total depth of the soil definition to the depth to bedrock. If regional maps of soil depth are not available, users are recommended to resort on Shangguan et al (2017).

References

Hengl T, Mendes de Jesus J, Heuvelink GBM, Ruiperez Gonzalez M, Kilibarda M, Blagotić A, et al. (2017) SoilGrids250m: Global gridded soil information based on machine learning. PLoS ONE 12(2): e0169748. doi:10.1371/journal.pone.0169748.

Poggio L, de Sousa LM, Batjes NH, Heuvelink GBM, Kempen B, Ribeiro E, Rossiter D (2021). SoilGrids 2.0: producing soil information for the globe with quantified spatial uncertainty. SOIL 7, 217-240. doi: 10.5194/soil-7-217-2021

Shangguan W, Hengl T, Mendes de Jesus J, Yuan H, Dai J (2017). Mapping the global depth to bedrock for land surface modeling. Journal of Advances in Modeling Earth Systems 9: 65-88. doi: 10.1002/2016MS000686

See also

add_topography(), impute_forests(), soil, defaultSoilParams

Author

Víctor Granda, EMF-CREAF

Miquel De Cáceres Ainsa, EMF-CREAF

Examples

 # \donttest{
   library(sf)
#> Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 8.2.1; sf_use_s2() is TRUE
   x <- st_sf(geometry = st_sfc(st_point(c(-5.6333, 42.6667)), crs = 4326))
   x_soil <- add_soilgrids(x, widths = c(300, 700, 1000))
#> ℹ Defining new column 'soil'
#> ✔ Defining new column 'soil' [5ms]
#> 
#> ℹ Querying 1 points to rest.isric.org:
#> ✔ Querying 1 points to rest.isric.org: [18ms]
#> 
   x_soil
#> Simple feature collection with 1 feature and 1 field
#> Geometry type: POINT
#> Dimension:     XY
#> Bounding box:  xmin: -5.6333 ymin: 42.6667 xmax: -5.6333 ymax: 42.6667
#> Geodetic CRS:  WGS 84
#> # A tibble: 1 × 2
#>            geometry soil        
#>         <POINT [°]> <list>      
#> 1 (-5.6333 42.6667) <df [3 × 7]>
   # See more complete examples in package vignettes 'Preparing inputs'
 # }