get.fluspect_mSCOPE

get.fluspect_mSCOPE is an adaptation of the Fluspect leaf model for the multi-layer (mSCOPE) canopy representation: leaf optical properties (reflectance, transmittance, fluorescence excitation-emission matrices Mb/Mf, and pigment contribution factors) are computed once per distinct leaf biochemistry profile layer (mly$nly layers), and then replicated across the nl canopy layers that fall within each profile layer, weighted by mly$pLAI.

Usage

get.fluspect_mSCOPE(
  mly,
  spectral,
  leafbio,
  soil,
  optipar,
  nl,
  step,
  get.plots = T
)

Arguments

mly

list. Multi-layer leaf biochemistry profile, with elements nly (number of distinct biochemistry layers), pLAI (LAI fraction of each layer), and per-layer biochemistry vectors pCab, pEWT, pCar, pLMA, pCs, pN (one value per layer, same units as the corresponding leafbio entries).

spectral

list. Spectral configuration, including wavelength vectors wlP, wlE, wlF, wlS and region boundaries reg1/reg2/reg3/IwlT.

leafbio

list. Baseline leaf biochemical/structural properties; the fields Cab, EWT, Car, LMA, Cs, N are overwritten per layer from mly.

soil

list. Soil properties; only rs_thermal (thermal-region soil reflectance) is used, and only for the optional diagnostic plots.

optipar

list. Leaf-level optical parameters used by the underlying Fluspect model.

nl

integer. Number of canopy layers over which the per-profile-layer leaf optics are replicated.

step

numeric, optional. Wavelength step (nm) used to compute the Mb/Mf excitation-emission matrices; if missing, a default step of 5 nm is used (matrix of 53 x 71), a step of 1 nm gives a 211 x 351 matrix. Must be lower than 8 nm.

get.plots

logical. If TRUE, produces diagnostic plots of leaf reflectance, pigment contribution factors, PSI/PSII quantum yield fractions and the Mb/Mf matrices. Default TRUE.

Value

A list leafopt with: refl/tran (leaf reflectance/transmittance per canopy layer x wavelength, [nl x length(wlP)]), kChlrel/kCarrel (relative contribution of chlorophyll/carotenoids to absorption, same dimensions), Mb/Mf (backward/forward fluorescence excitation-emission matrices, replicated per canopy layer), phiI/phiII (PSI/PSII relative quantum yield spectra at the fluorescence wavelengths).

Author

Christiaan van der Tol  (Original version in Matlab)

Carlos Camino (Ported version into R)

Examples

if (FALSE) { # \dontrun{
leafopt <- get.fluspect_mSCOPE(mly, spectral, leafbio, soil, optipar, nl,
                                step = 5, get.plots = FALSE)
} # }