fetchSoilGrids: Get SoilGrids 2.0 Property Estimates for Points or Spatial...

In soilDB: Soil Database Interface

Get SoilGrids 2.0 Property Estimates for Points or Spatial Extent

Description

This function obtains SoilGrids 2.0 properties information (250m raster resolution) given a data.frame containing site IDs, latitudes and longitudes, or a spatial extent (see grid=TRUE argument).

Usage

fetchSoilGrids(
  x,
  loc.names = c("id", "lat", "lon"),
  depth_intervals = c("0-5", "5-15", "15-30", "30-60", "60-100", "100-200"),
  variables = c("bdod", "cec", "cfvo", "clay", "nitrogen", "phh2o", "sand", "silt",
    "soc", "ocd", "wv0010", "wv0033", "wv1500"),
  grid = FALSE,
  filename = NULL,
  overwrite = TRUE,
  target_resolution = c(250, 250),
  summary_type = c("Q0.05", "Q0.5", "Q0.95", "mean"),
  endpoint = ifelse(!grid, "https://rest.isric.org/soilgrids/v2.0/properties/query",
    "https://files.isric.org/soilgrids/latest/data/"),
  ...,
  verbose = FALSE,
  progress = FALSE
)

Arguments

x	A data.frame containing 3 columns referring to site ID, latitude and longitude. Or a spatial (sf, terra) object for which a bounding box can be calculated when grid=TRUE.
loc.names	Optional: Column names referring to site ID, latitude and longitude. Default: c("id", "lat", "lon")
depth_intervals	Default: "0-5", "5-15", "15-30", "30-60", "60-100", "100-200"
variables	Default: "bdod", "cec", "cfvo", "clay", "nitrogen", "phh2o", "sand", "silt", "soc", "ocd", "wv0010", "wv0033", "wv1500". Optionally "ocs" (only for 0 to 30 cm interval).
grid	Download subset of SoilGrids Cloud Optimized GeoTIFF? Default: FALSE
filename	Only used when grid=TRUE. If NULL defaults to an in-memory raster, or temporary file if result does not fit in memory.
overwrite	Only used when grid=TRUE. Default: FALSE
target_resolution	Only used when grid=TRUE. Default: c(250, 250) (250m x 250m pixels)
summary_type	Only used when grid=TRUE. One or more of "Q0.05", "Q0.5", "Q0.95", "mean"; these are summary statistics that correspond to 5th, 50th, 95th percentiles, and mean value for selected variables.
endpoint	Optional: custom API endpoint. Default: "https://rest.isric.org/soilgrids/v2.0/properties/query" when grid=FALSE; "https://files.isric.org/soilgrids/latest/data/" when grid=TRUE.
...	Additional arguments passed to terra::writeRaster() when grid=TRUE.
verbose	Print messages? Default: FALSE
progress	logical, give progress when iterating over multiple requests; Default: FALSE

Details

SoilGrids API and maps return values as whole (integer) numbers to minimize the storage space used. These values have conversion factors applied by fetchSoilGrids() to produce conventional units shown in the table below (see Details).

Properties

Name	Description	Mapped units	Conversion factor	Conventional units
bdod	Bulk density of the fine earth fraction	cg/cm^3	100	kg/dm^3
cec	Cation Exchange Capacity of the soil	mmol(c)/kg	10	cmol(c)/kg
cfvo	Volumetric fraction of coarse fragments (> 2 mm)	cm^3/dm^3 (vol per mil)	10	cm^3/100cm^3 (vol%)
clay	Proportion of clay particles (< 0.002 mm) in the fine earth fraction	g/kg	10	g/100g (%)
nitrogen	Total nitrogen (N)	cg/kg	100	g/kg
phh2o	Soil pH	pH*10	10	pH
sand	Proportion of sand particles (> 0.05 mm) in the fine earth fraction	g/kg	10	g/100g (%)
silt	Proportion of silt particles (>= 0.002 mm and <= 0.05 mm) in the fine earth fraction	g/kg	10	g/100g (%)
soc	Soil organic carbon content in the fine earth fraction	dg/kg	10	g/kg
ocd	Organic carbon density	hg/m^3	10	kg/m^3
ocs	Organic carbon stocks (0-30cm depth interval only)	t/ha	10	kg/m^2
wv0010	Volumetric Water Content at 10kPa	0.1 v% or 1 mm/m	10	volume (%)
wv0033	Volumetric Water Content at 33kPa	0.1 v% or 1 mm/m	10	volume (%)
wv1500	Volumetric Water Content at 1500kPa	0.1 v% or 1 mm/m	10	volume (%)

SoilGrids predictions are made for the six standard depth intervals specified in the GlobalSoilMap IUSS working group and its specifications. The default depth intervals returned are (in centimeters): "0-5", "5-15", "15-30", "30-60", "60-100", "100-200" for the properties "bdod", "cec", "cfvo", "clay", "nitrogen", "phh2o", "sand", "silt", "soc", "ocd", "wv0010", "wv0033", "wv1500"–each with 5th, 50th, 95th, mean and uncertainty values. Soil organic carbon stocks (0-30cm) (variables="ocs") are returned only for depth_intervals="0-30". The uncertainty values are the ratio between the inter-quantile range (90% prediction interval width) and the median : (Q0.95-Q0.05)/Q0.50. All values are converted from "mapped" to "conventional" based on above table conversion factors. Point data requests are made through "properties/query" endpoint of the SoilGrids v2.0 REST API. Please check ISRIC's data policy, disclaimer and citation: https://www.isric.org/about/data-policy.

Find out more information about the SoilGrids and GlobalSoilMap products here:

• https://www.isric.org/explore/soilgrids/faq-soilgrids

• https://www.isric.org/sites/default/files/GlobalSoilMap_specifications_december_2015_2.pdf

Value

A SoilProfileCollection or SpatRaster when grid=TRUE. Returns try-error if all requests fail. Any error messages resulting from parsing will be echoed when verbose=TRUE.

Author(s)

Andrew G. Brown

References

• Common soil chemical and physical properties: Poggio, L., de Sousa, L. M., Batjes, N. H., Heuvelink, G. B. M., Kempen, B., Ribeiro, E., and Rossiter, D.: SoilGrids 2.0: producing soil information for the globe with quantified spatial uncertainty, SOIL, 7, 217–240, 2021. DOI: \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.5194/soil-7-217-2021")}

• Soil water content at different pressure heads: Turek, M.E., Poggio, L., Batjes, N. H., Armindo, R. A., de Jong van Lier, Q., de Sousa, L.M., Heuvelink, G. B. M. : Global mapping of volumetric water retention at 100, 330 and 15000 cm suction using the WoSIS database, International Soil and Water Conservation Research, 11-2, 225-239, 2023. DOI: \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1016/j.iswcr.2022.08.001")}

Examples

## Not run: 
  library(aqp)
  
  your.points <- data.frame(id  = c("A", "B"), 
                           lat = c(37.9, 38.1), 
                           lon = c(-120.3, -121.5), 
                           stringsAsFactors = FALSE)
  x <- try(fetchSoilGrids(your.points))
 
  if (!inherits(x, 'try-error'))
   aqp::plotSPC(x, name = NA, color = "socQ50")
 
  # organic carbon stocks use 0-30cm interval
  y <- try(fetchSoilGrids(your.points[1, ], 
                          depth_interval = c("0-5", "0-30", "5-15", "15-30"),
                          variables = c("soc", "bdod", "ocd", "ocs")))
                          
  # extract horizons from a SoilProfileCollection where horizon 2 overlaps 1, 3, and 4
  h <- aqp::horizons(y)
  
  # "ocs" (organic carbon stock 0-30cm interval)
  h[2, ]
  
  h$thickness_meters <- ((h$hzdepb - h$hzdept) / 100)

  # estimate "ocs" from modeled organic carbon and bulk density in 0-5, 5-15, 15-30 intervals
  #  (sum the product of soc, bdod, and thickness in meters)
  #  (1 gram per cubic decimeter = 1 kilogram per cubic meter)
  sum(h$socmean * h$bdodmean * h$thickness_meters, na.rm = TRUE)
  
  # estimate "ocs" from modeled organic carbon density in 0-5, 5-15, 15-30 intervals
  #  (sum the product of "ocd" and thickness in meters)
  sum(h$ocdmean * h$thickness_meters, na.rm = TRUE)
 

## End(Not run)

soilDB documentation built on Sept. 11, 2024, 8:28 p.m.