fetchSoilGrids: Get SoilGrids 250m properties information from point...

In soilDB: Soil Database Interface

Get SoilGrids 250m properties information from point locations

Description

This function obtains SoilGrids properties information (250m raster resolution) given a data.frame containing site IDs, latitudes and longitudes. SoilGrids API and maps return values as whole (integer) numbers to minimize the storage space used. These values are converted by to produce conventional units by 'fetchSoilGrids()“

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"),
  verbose = FALSE,
  progress = FALSE
)

Arguments

x	A data.frame containing 3 columns referring to site ID, latitude and longitude.
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"
verbose	Print messages? Default: FALSE
progress	logical, give progress when iterating over multiple requests; Default: FALSE

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

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"–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

Author(s)

Andrew G. Brown

References

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. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.5194/soil-7-217-2021")}

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 Nov. 17, 2023, 1:09 a.m.