Build PedonRecords with attached Vis-NIR/MIR spectra from a table

Groups a reflectance + metadata table by profile and returns one PedonRecord per profile, with each profile's sample rows stacked into $spectra$vnir (rows = horizons, cols = wavelengths) and the lab attributes / depths written to the horizons. Taxonomic labels are stored in $site (reference_wrb / reference_sibcs / reference_st). These pedons are the query objects for classify_*(gapfill = list(method = "spectra", ossl_library = <lib>)).

Usage

pedons_from_spectral_table(
  reflectance,
  metadata,
  id_col = "id",
  profile_col = NULL,
  wavelengths = NULL,
  resample_to = NULL,
  property_map = NULL,
  label_map = NULL,
  normalize = c("auto", "none", "percent"),
  keep_properties = FALSE,
  verbose = TRUE
)

Arguments

reflectance

Reflectance data: a matrix / data.frame with rows = samples and columns named by wavelength (nm); OR a long data.frame with id_col, wavelength_nm, reflectance; OR a path to a CSV in either form.

metadata

A data.frame with one row per sample carrying id_col plus lab attributes and optional taxonomic labels and lat/ lon. Rows are aligned to reflectance by id_col.

id_col

Sample identifier column shared by both tables (default "id").

profile_col

Column grouping samples into profiles (default id_col: one profile per sample, e.g. a topsoil library).

wavelengths

Optional explicit wavelength vector (nm) when the reflectance columns are not wavelength-named.

resample_to

Optional target wavelength grid (nm) to linearly resample every spectrum onto (e.g. 350:2500); default keeps the native grid.

property_map, label_map

Optional named lists overriding the alias auto-detection, e.g. property_map = list(clay_pct = "ARGILA").

normalize

One of "auto" (divide by 100 when values look like percent), "percent", or "none".

keep_properties

If TRUE, also write the mapped lab attributes to the horizons (default FALSE – a field pedon usually has only the scan, which is the scenario the spectral fill targets).

verbose

Print a one-line summary (default TRUE).

Value

A list of PedonRecord objects.

See also

read_spectral_library, benchmark_spectral_fill