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Run the LUCAS Soil 2018 / ESDB WRB benchmark

Source: R/benchmark-lucas-2018.R
benchmark_lucas_2018.Rd

For each pedon in pedons, attaches the canonical Reference Soil Group at its coordinate via lookup_esdb, runs classify_wrb2022 (or classify_sibcs), and tabulates predicted vs reference. Optionally fills missing texture from ISRIC SoilGrids 250m before classifying so that WRB diagnostic horizons that depend on clay (argic, ferralic, nitic) are reachable.

Usage

benchmark_lucas_2018(
  pedons,
  esdb_root,
  attribute = "WRBLV1",
  fill_texture_from = NULL,
  fill_topsoil_from = c("none", "soilgrids", "spectra"),
  fill_subsoil_from = c("none", "soilgrids"),
  fill_properties = c("clay", "sand", "silt", "phh2o", "soc", "cec", "bdod", "nitrogen",
    "cfvo"),
  ossl_models = NULL,
  classify_with = c("wrb2022", "sibcs"),
  max_n = NULL,
  soilgrids_lookup_fn = lookup_soilgrids,
  verbose = TRUE
)

Arguments

pedons

List of PedonRecord objects, typically from load_lucas_soil_2018.

esdb_root

Path to the unpacked ESDB raster directory (containing the WRBLV1/ sub-folder).

attribute

ESDB attribute to use as reference. Default "WRBLV1" (Reference Soil Group, 31 codes). Other sensible choices: "FAO90LV1" (legacy FAO 1990).

fill_texture_from

Deprecated alias for fill_topsoil_from (v0.9.49 signature). When "soilgrids", treated as fill_topsoil_from = "soilgrids" with fill_properties = c("clay", "sand", "silt") and fill_subsoil_from = "none".

fill_topsoil_from

One of "none" (default), "soilgrids" (fills topsoil 0-20 cm from SoilGrids 250m at 0-5 cm), or "spectra" (runs predict_from_spectra with the supplied ossl_models; pedons must have $spectra$vnir attached, e.g. via attach_lucas_spectra).

fill_subsoil_from

One of "none" (default) or "soilgrids" (synthesises a 30-60 cm B horizon from SoilGrids 250m). Unlocks WRB diagnostic horizons that depend on subsoil features (cambic, argic, mollic).

fill_properties

Character vector of SoilGrids properties to fill when fill_topsoil_from = "soilgrids" or fill_subsoil_from = "soilgrids". Default uses all 9 properties: clay, sand, silt, phh2o, soc, cec, bdod, nitrogen, cfvo. Set to c("clay", "sand", "silt") to recover the v0.9.49 behaviour. cfvo is mapped to coarse_fragments_pct, which drives the Leptosols diagnostic (>= 90 within 25 cm).

ossl_models

Required when fill_topsoil_from = "spectra". A list of soilKey_pls_model objects from train_pls_from_ossl (v0.9.46).

classify_with

One of "wrb2022" (default) or "sibcs".

max_n

Optional integer cap on the number of pedons benchmarked. Useful for quick development runs.

soilgrids_lookup_fn

Internal: SoilGrids lookup function (defaults to lookup_soilgrids). Override for unit tests to inject a deterministic stub.

verbose

If TRUE (default), prints progress.

Value

A list with elements:

predictions

data.frame with one row per pedon: point_id, lon, lat, country, predicted, reference_code, reference_name, agree.

confusion

Confusion table (predicted vs reference) over in-scope rows.

accuracy

Overall fraction of correct classifications among in-scope rows.

per_rsg

Per-RSG recall data.frame.

n_in_scope

Number of pedons with both predicted and reference set.

n_total

Total pedons benchmarked.

n_errors

Number of pedons where the classifier errored out.

errors

List of (i, id, error) tuples for classifier errors.

config

Recap of arguments used.

Details

This closes Route B of the v0.9.27 EU-LUCAS roadmap end-to-end: v0.9.44 lookup_esdb provides the reference label; v0.9.49 (this) provides the loader and the comparison loop; v0.9.48 lookup_soilgrids fills texture; v0.9.46 predict_from_spectra and v0.9.47 predict_munsell_from_spectra can fill the chemistry / Munsell gaps when Vis-NIR is available.

See also

load_lucas_soil_2018, lookup_esdb, lookup_soilgrids.

Examples

if (FALSE) { # \dontrun{
pedons <- load_lucas_soil_2018(
  "soil_data/eu_lucas/LUCAS-SOIL-2018-data-report-readme-v2/LUCAS-SOIL-2018-v2",
  countries = c("ES"), max_n = 50)
bench <- benchmark_lucas_2018(
  pedons,
  esdb_root = "soil_data/eu_lucas/ESDB-Raster-Library-1k-GeoTIFF-20240507",
  fill_texture_from = "soilgrids")
bench$accuracy
bench$per_rsg
} # }