prospect
in forward modeThe function PROSPECT
runs PROSPECT for individual samples and expects the following input variables.
SpecPROSPECT
: dataframe including the refractive index and specific absorption ceofficients, defined for a given spectral range (max range: 400 nm - 2500 nm). simulation and inversion on different spectral domains can be peformed by adapting the information in SpecPROSPECT
N
(default = 1.5)CHL
(default = 40.0 \(\mu g.cm^2\))CAR
(default = 8.0 \(\mu g.cm^2\))ANT
(default = 0.0 \(\mu g.cm^2\))BROWN
(default = 0.0 arbitrary units)EWT
(default = 0.01 \(g.cm^2\))LMA
(default = 0.008 \(g.cm^2\))PROT
(default = 0.0 \(g.cm^2\))CBC
(default = 0.0 \(g.cm^2\))alpha
(default = 40.0 degrees)PROSPECT
returns a list containing directional-hemispherical reflectance and transmittance (reflectance
and transmittance
) corresponding to the input variables, and the corresponding wavelengths in the list element wvl
.
Default values are set for undeclared parameters
Following the same definition of the input parameters, user only has to adjust the spectral range from SpecPROSPECT
. SpecPROSPECT$lambda
contains the spectral bands for the different optical constants.
# define the spectral range for simulations in the VNIR from 400 to 1000 nm
# identify closest spectral bands to the boundaries
# (please adjust if you need strict inclusion / excusion of bands)
wvlRange = list()
wvlRange$lb <- which(abs(SpecPROSPECT$lambda-400)==min(abs(SpecPROSPECT$lambda-400)))
wvlRange$ub <- which(abs(SpecPROSPECT$lambda-1000)==min(abs(SpecPROSPECT$lambda-1000)))
SpecPROSPECT_VNIR <- SpecPROSPECT[wvlRange$lb:wvlRange$ub,]
LRT_VNIR <- PROSPECT(SpecPROSPECT_VNIR,N = 1.4,CHL = 30,CAR = 6,EWT = 0.02,LMA = 0.01)
PROSPECT-PRO is the latest official version released. However, you may not be interested in all these input biochemical constituents.
Still, we recommend using PROSPECT-PRO and selecting the constituents of interest, performances should correspond to your expectations.
The only difference between PROSPECT-PRO and PROSPECT-D is that LMA is divided into proteins and CBC. Therefore, the default values in prospect
correspond to calling PROSPECT-D, as PROT
and CBC
are set to 0. Keep in mind that either LMA
or PROT
and CBC
should be set to 0. A message will be displayed if it is not the case:
'PROT and/or CBC are not set to 0
LMA is not set to 0 neither, which is physically incorrect
(LMA = PROT + CBC)
We assume that PROSPECT-PRO was called and set LMA to 0
Please correct input parameters LMA, PROT and/or CBC if needed'
Here is an example to run PROSPECT-D:
CHL <- 45; CAR <- 10; ANT <- 0.2
EWT <- 0.012; LMA <- 0.010; N <- 1.3
LRT_D <- PROSPECT(SpecPROSPECT,CHL=CHL,CAR=CAR,ANT=ANT,EWT=EWT,LMA=LMA,N=N)
and another one with PROSPECT-PRO, which should lead to very similar leaf optics:
CHL <- 45; CAR <- 10; ANT <- 0.2
EWT <- 0.012; LMA <- 0.000; N <- 1.3
PROT <- 0.001; CBC <- 0.009;
LRT_PRO <- PROSPECT(SpecPROSPECT,CHL=CHL,CAR=CAR,ANT=ANT,EWT=EWT,PROT=PROT,CBC=CBC,N=N)
while using proteins only instead of proteins + CBC to simulate LMA leads to different results:
CHL <- 45; CAR <- 10; ANT <- 0.2
EWT <- 0.012; LMA <- 0.000; N <- 1.3
PROT <- 0.010; CBC <- 0.000;
LRT_PRO2 <- PROSPECT(SpecPROSPECT,CHL=CHL,CAR=CAR,ANT=ANT,EWT=EWT,PROT=PROT,CBC=CBC,N=N)
On the other hand, using CBC only instead of proteins + CBC to simulate LMA leads to very similar results compared to simulation with PROSPECT-D.
This is explained by the low proportion of poteins compared to CBC in he total comntribution to LMA, and the very similar specific absorption coefficient between LMA and CBC. This also highlights the challenges for the proper estimation of proteines from LOP.
CHL <- 45; CAR <- 10; ANT <- 0.2
EWT <- 0.012; LMA <- 0.000; N <- 1.3
PROT <- 0.000; CBC <- 0.010;
LRT_PRO3 <- PROSPECT(SpecPROSPECT,CHL=CHL,CAR=CAR,ANT=ANT,EWT=EWT,PROT=PROT,CBC=CBC,N=N)
If you want to run previous versions of PROSPECT:
We do not recommend using PROSPECT-4 or PROSPECT-5, as the calibration of the refractive index along with specific absorption coefficients for chlorophyls and carotenoids resulted in artifacts in the VIS domain.
However if you are not interested in anthocyanins, the default value for ANT
is 0.0, so simulating leaf optics without ANT
should do the job.
If you do not want to differentiate chlorophylls and carotenoids, we recommend that you use PROSPECT-PRO and set CAR
as a constant fraction of CHL
.
prospect
Look-Up-Tables (LUT) are widely used in order to infer leaf charactristics from PROSPECT, based on minimization techniques. The function PROSPECT_LUT
allows computation of a LUT directly based on a list of input parameters.
The following example produces a LUT with the function PROSPECT_LUT
of prospect
. Undefined parameters are set to their default value; Vectors of values are expected to be the same length.