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Build a canopy-model-ready soil reflectance spectrum from MARMIT

get.marmit.rsoil.Rd

High-level wrapper around get.marmit1/get.marmit2 that loads the measured dry-soil reference spectrum and water-optics constants bundled with ToolsRTM, runs the MARMIT model, and resamples the result onto a fixed wavelength grid so it can be dropped straight into rsoil for foursail, foursail2, inform, or into SPART's rsoil override.

Usage

get.marmit.rsoil(
  database = "Bablet_2016",
  id = 1,
  version = "marmit1",
  L = 0.05,
  eps = 0.3,
  n_i = 1.53,
  k_i = 0.001,
  d_i = 5e-04,
  wl.out = 400:2500,
  db_root = NULL
)

Arguments

database

character. Soil database name (a folder under extdata/marmit/databases/). Default "Bablet_2016", the only one bundled.

id

integer. Soil ID within the database's index CSV (see the ID column). Default 1.

version

character. "marmit1" (default) or "marmit2". MARMIT-2 additionally accounts for soil particle size/refractive index (n_i/k_i/d_i) and is generally more accurate for coarser soils; MARMIT-1 is simpler and matches the original 2018 paper.

L

numeric. Thickness of the surface water layer, cm. Default 0.05.

eps

numeric (0-1). Fraction of the soil surface that is wet. Default 0.3.

n_i, k_i, d_i

numeric. MARMIT-2-only soil-particle parameters (real refractive index, imaginary refractive index, particle volume fraction). Ignored when version = "marmit1". Defaults (1.53, 0.001, 0.0005) match the MARMIT Shiny app's defaults.

wl.out

integer vector. Wavelength grid (nm) the output is resampled/padded onto. Default 400:2500 (matches foursail's spectrum.all = TRUE / inform grid); pass 400:2400 for Fluspect-leaf-model calls to foursail/foursail2.

db_root

character or NULL. Directory containing database subfolders (e.g. "databases" at the RTM-Suite repo root, which has all 8 MARMIT databases – see Details). When NULL (default), only the bundled Bablet_2016 database is available.

Value

A list:

wavelength

the wl.out grid.

rsoil.dry

dry-soil reflectance on wl.out (no MARMIT wetting applied – the raw measured reference).

rsoil.wet

MARMIT-simulated reflectance on wl.out, ready to use as rsoil.

SMC

estimated gravimetric soil moisture content (percent), from sigmoid.soil.

params

a one-row data.frame recording database, id, version, L, eps, n_i, k_i, d_i.

Details

Only the Bablet 2016 soil database (Bablet et al., 2018) is bundled with the package, to keep install size small. The other 7 MARMIT databases (Dupiau 2020, Humper 2015, Lesaignoux 2008, Liu 2002, Lobell 2002, Marcq 2012, Philpot 2014 – see https://pss-gitlab.math.univ-paris-diderot.fr/marmit/marmit) ship in the RTM-Suite monorepo's own databases/ folder (repo root, one subfolder per database, ~200MB total – too large to bundle in the package itself). Point at it directly with db_root, e.g. get.marmit.rsoil(database = "Liu_2002", db_root = "databases") run from the repo root – no copying required. Any other folder with the same layout (an index CSV <name>/<name>.csv with columns ID, Refl_file, SMCg, K, a, psi – extra columns are ignored – plus <name>/spectra/<Refl_file> tab-separated Wvl,R files) works the same way. Leaving db_root = NULL (the default) keeps the original behavior: only the bundled Bablet_2016 database, looked up under system.file("extdata", "marmit", "databases", package = "ToolsRTM").

The dry-soil reference for a given id is the driest spectrum on file for that soil (the row with the smallest SMCg), matching how the original MARMIT Shiny app selects it. Wavelengths beyond the native range of that spectrum (some databases stop at 2400 or 2490nm, not 2500) are held constant at the last available value – the same boundary behavior SPART uses for its own BSM soil beyond 2400nm.

See also

get.marmit1, get.marmit2

Examples

if (FALSE) { # \dontrun{
soil <- get.marmit.rsoil(database = "Bablet_2016", id = 1, L = 0.05, eps = 0.3)
plot(soil$wavelength, soil$rsoil.wet, type = "l")
lines(soil$wavelength, soil$rsoil.dry, col = "grey50")

# Feed straight into fourSAIL (PROSPECT-D domain, full 400-2500nm)
LUT <- as.data.frame(getLUT(inputs = ToolsRTM::inputsPROSAIL, nLUT = 1, setseed = 1))
sim <- foursail(inputLUT = LUT, rsoil = soil$rsoil.wet, LeafModel = "PROSPECT-D")

# Any of the other 7 databases, from the RTM-Suite repo's own databases/ folder
# (run from the repo root, or pass an absolute path):
soil2 <- get.marmit.rsoil(database = "Liu_2002", id = 1, db_root = "databases")
} # }