| Title: | Fluspect-B |
|---|---|
| Description: | A model for leaf fluorescence, reflectance and transmittance spectra. It implements the model introduced by Vilfan et al. (2016) <DOI:10.1016/j.rse.2016.09.017>. Fluspect-B calculates the emission of ChlF on both the illuminated and shaded side of the leaf. Other input parameters are chlorophyll and carotenoid concentrations, leaf water, dry matter and senescent material (brown pigments) content, leaf mesophyll structure parameter and ChlF quantum efficiency for the two photosystems, PS-I and PS-II. |
| Authors: | Alberto Hornero, Nastassia Vilfan, Christiaan van der Tol, Onno Muller, Uwe Rascher, Wouter Verhoef |
| Maintainer: | Alberto Hornero <[email protected]> |
| License: | GPL-3 |
| Version: | 1.0.0 |
| Built: | 2024-11-08 06:13:46 UTC |
| Source: | https://github.com/cran/fluspect |
define.bands defines the spectral regions for the Fluspect-B model
define.bands()define.bands()
Define spectral regions for SCOPE v_1.40
All spectral regions are defined here as row vectors
WV Jan. 2013
a spectral object.
Nastassia Vilfan, Christiaan van der Tol, Onno Muller, Uwe Rascher, Wouter Verhoef (Original version in Matlab)
Alberto Hornero (Ported version into R)
spectral <- define.bands()spectral <- define.bands()
fluspect calculates reflectance and transmittance spectra of a leaf using FLUSPECT-B,
plus four excitation-fluorescence matrices
fluspect(leafbio, spectral = define.bands(), optipar = NULL)fluspect(leafbio, spectral = define.bands(), optipar = NULL)
leafbio |
Data Frame. It contains: Cab, Cca, Cw, Cdm, Cs, N, fqe |
spectral |
List. (Optional) A spectral object created with define.bands. A default spectral object is used if the user does not indicate any. |
optipar |
Data Frame. (Optional) It contains: nr, Kdm, Kab, Kca, Kw, Ks, phiI, phiII. A default optipar object is used if the user does not indicate any. |
More information: Fluspect-B: A model for leaf fluorescence, reflectance and transmittance spectra. Vilfan et al., 2016
Original version in MatLab: github.com/Christiaanvandertol/Fluspect
a list which contains:
refl (reflectance)
tran (transmittance)
Mb (backward scattering fluorescence matrix, I for PSI and II for PSII)
Mf (forward scattering fluorescence matrix, I for PSI and II for PSII)
Nastassia Vilfan, Christiaan van der Tol, Onno Muller, Uwe Rascher, Wouter Verhoef (Original version in Matlab)
Alberto Hornero (Ported version into R)
leafbio <- data.frame(Cab = 70, Cca = 30, Cw = 0.013, Cdm = 0.024, Cs = 0.0, N = 4.09, fqe = 0.02) leafopt <- fluspect(leafbio) plot(leafopt$refl)leafbio <- data.frame(Cab = 70, Cca = 30, Cw = 0.013, Cdm = 0.024, Cs = 0.0, N = 4.09, fqe = 0.02) leafopt <- fluspect(leafbio) plot(leafopt$refl)
write.leafopt writes the leafopt object as text files
write.leafopt(leafopt, path, digits = 5)write.leafopt(leafopt, path, digits = 5)
leafopt |
List. Spectral object generated with fluspect |
path |
String. Output path. If the directory does not exist, a new one will be created. |
digits |
Integer. (Optional) Number of digits (by default 5) |
It always writes the text files in UNIX format, under the specified output path. It will override if files already exists. The output filenames are:
leafoptrefl.txt
leafopttran.txt
leafoptkChlrel.txt
leafoptMbI.txt
leafoptMbII.txt
leafoptMfI.txt
leafoptMbII.txt
Alberto Hornero
leafbio <- data.frame(Cab = 70, Cca = 30, Cw = 0.013, Cdm = 0.024, Cs = 0.0, N = 4.09, fqe = 0.02) leafopt <- fluspect(leafbio) write.leafopt(leafopt, path = file.path(tempdir(), 'output'))leafbio <- data.frame(Cab = 70, Cca = 30, Cw = 0.013, Cdm = 0.024, Cs = 0.0, N = 4.09, fqe = 0.02) leafopt <- fluspect(leafbio) write.leafopt(leafopt, path = file.path(tempdir(), 'output'))