Fill missing soil attributes from spectra via OSSL

Given a PedonRecord carrying a spectra$vnir matrix (rows = horizons, columns = wavelengths in nm), pre-processes the spectra, predicts the requested soil properties using the chosen OSSL-backed method, and writes the predictions into the pedon's horizons table via pedon$add_measurement(..., source = "predicted_spectra"). Each call updates the pedon's provenance log so that downstream classification can derive an evidence grade.

Usage

fill_from_spectra(
  pedon,
  library = "ossl",
  region = c("global", "south_america", "north_america", "europe", "africa"),
  properties = c("clay_pct", "sand_pct", "silt_pct", "cec_cmol", "bs_pct", "ph_h2o",
    "oc_pct", "fe_dcb_pct", "caco3_pct"),
  method = c("mbl", "plsr_local", "pretrained"),
  preprocess = "snv+sg1",
  k_neighbors = 100L,
  overwrite = FALSE,
  ossl_library = getOption("soilKey.ossl_library"),
  ossl_models = getOption("soilKey.ossl_models"),
  verbose = TRUE
)

Arguments

pedon

A PedonRecord with a spectra$vnir matrix.

library

Currently only "ossl" is supported.

region

One of "global", "south_america", "north_america", "europe", "africa". Used to subset the OSSL training data when supported by the underlying backend.

properties

Character vector of OSSL-supported property names to predict. Default covers the most-requested WRB/SiBCS-relevant attributes.

method

One of "mbl", "plsr_local", "pretrained".

preprocess

Pre-processing pipeline; passed to preprocess_spectra.

k_neighbors

Number of neighbours for memory-based methods.

overwrite

If FALSE (default), only fill cells whose existing provenance is weaker than predicted_spectra.

ossl_library

Optional OSSL library object (see predict_ossl_mbl). Defaults to getOption("soilKey.ossl_library"), so a library set once reaches every call, including gap-fill from classify_all(gapfill = list(method = "spectra")). Without one the predictions are synthetic placeholders.

ossl_models

Optional named list of pretrained models (see predict_ossl_pretrained). Defaults to getOption("soilKey.ossl_models").

verbose

If TRUE, prints a cli summary.

Value

The mutated pedon, invisibly. Provenance entries with source = "predicted_spectra" are added per (horizon, property).

Details

By default, predicted values do not overwrite measured values (the add_measurement() authority logic protects them). Setting overwrite = TRUE forces overwrite of any non-measured value.

See also

preprocess_spectra, predict_ossl_mbl, predict_ossl_plsr_local, predict_ossl_pretrained, pi_to_confidence.