Read one WoSIS profile's layers live from ISRIC

Fetches the layers of a single profile from ISRIC's WoSIS GraphQL endpoint and returns them in the soilKey horizon schema. Nothing is written to disk.

Usage

read_wosis_layers_graphql(
  profile_id,
  timeout = 30,
  max_layers = 40L,
  page_size = 10L,
  progress = NULL
)

Arguments

profile_id

A WoSIS profile_id, as returned by read_wosis_profiles_graphql.

timeout

Seconds to wait for each request (default 30).

max_layers

Largest profile, in layers, that is read (default 40).

page_size

Layers per request (default 10).

progress

Optional function(done, total) called after each page, for a progress bar.

Value

A data.frame of horizons in the soilKey schema, top to bottom, with attributes "provenance" (one row per value: horizon, column, WoSIS code, unit and method), "licence" (the most restrictive licence among the layers), "dataset", "n_layers" and "depth_shift_cm" (non-zero when depths were shifted so an organic surface layer starts at 0 cm). Zero rows, with a "wosis_error" attribute, when ISRIC cannot be reached, the profile has no layers, or it has more than max_layers.

Details

Units are converted from ISRIC's own catalogue (organic carbon, total nitrogen and carbonate equivalent arrive in g/kg and become %), and only properties whose method matches the soilKey column are mapped: volumetric coarse fragments, saturated-paste EC, gravimetric water retention and CEC at pH 7. WoSIS serves no exchangeable bases, base saturation or Fe/Al oxides, so those columns stay empty and the classifier reports them as missing.

Load on ISRIC

The endpoint is a free public service whose database cancels any statement that runs longer than about 30 seconds, and the cost of a query grows with the number of layers times the number of properties. The layers are therefore counted first with a cheap query, then read in pages of page_size in a stable order. Profiles recorded as many fine depth increments (some have 90 one-centimetre layers) exceed max_layers and are not read unless you raise it deliberately.

See also

wosis_profile_to_pedon, wosis_citation.

Examples

# \donttest{
# Needs network access; skipped offline and in batch checks.
online <- interactive() && requireNamespace("httr", quietly = TRUE) &&
  !inherits(try(httr::HEAD("https://graphql.isric.org", httr::timeout(5)),
                silent = TRUE), "try-error")
if (online) {
  p <- read_wosis_profiles_graphql(country = "Argentina", n_max = 1)
  if (nrow(p)) {
    h <- read_wosis_layers_graphql(p$profile_id[1])
    h[, c("top_cm", "bottom_cm", "designation", "clay_pct", "oc_pct")]
  }
}
# }