Merge branch 'dev'

R/Lib_PROSPECT.R

@@ -197,14 +197,14 @@ check_version_prospect <- function(LMA, PROT, CBC){
 #' This function adapts SpecPROSPECT accordingly to experimental data
 #' or to a spectral domain defined by UserDomain
 #' @param lambda numeric. Spectral bands corresponding to experimental data
-#' @param SpecPROSPECT list. Includes optical constants
-#' refractive index, specific absorption coefficients and corresponding spectral bands
+#' @param SpecPROSPECT list. Includes optical constants: refractive index,
+#' specific absorption coefficients and corresponding spectral bands
 #' @param Refl numeric. Measured reflectance data
 #' @param Tran numeric. Measured Transmittance data
-#' @param UserDomain numeric. either Lower and upper bounds for domain of interest (optional)
-#' or list of spectral bands of interest
-#' @param UL_Bounds boolean. set to TRUE if UserDomain only includes lower and upper band,
-#' set to FALSE if UserDomain is a list of spectral bands (in nm)
+#' @param UserDomain numeric. either Lower and upper bounds for domain of
+#' interest (optional) or list of spectral bands of interest
+#' @param UL_Bounds boolean. set to TRUE if UserDomain only includes lower and
+#' upper band, set to FALSE if UserDomain is a list of spectral bands (in nm)
 #'
 #' @return list including spectral properties at the new resolution
 #' @import dplyr
@@ -248,9 +248,9 @@ FitSpectralData <- function(lambda, SpecPROSPECT = NULL,
 #' computation of a LUT of leaf optical properties using a set of
 #' leaf chemical & structural parameters
 #'
+#' @param Input_PROSPECT dataframe. list of PROSPECT input parameters.
 #' @param SpecPROSPECT list. spectral constants
 #' refractive index, specific absorption coefficients & spectral bands
-#' @param Input_PROSPECT dataframe. full list of PROSPECT input parameters. Default = Set to NULL
 #'
 #' @return list. LUT including leaf reflectance and transmittance
 #' @export

R/SpecPROSPECT_FullRange-data.R

@@ -20,6 +20,8 @@
 #'  - *SAC_LMA*: specific absorption coefficient for dry matter (Leaf Mass per Area)
 #'  - *SAC_PROT*: specific absorption coefficient for proteins
 #'  - *SAC_CBC*: specific absorption coefficient for carbon-base constituents
-#'  - *calctav_90*: transmissivity of a dielectric plane surface, averaged over all directions of incidence and over all polarizations for solid angle of 90 degrees
-#'  - *calctav_40*: transmissivity of a dielectric plane surface, averaged over all directions of incidence and over all polarizations for solid angle of 40 degrees
+#'  - *calctav_90*: transmissivity of a dielectric plane surface, averaged over
+#'  all directions of incidence & all polarizations for solid angle of 90 deg
+#'  - *calctav_40*: transmissivity of a dielectric plane surface, averaged over
+#'  all directions of incidence & all polarizations for solid angle of 40 deg
 "SpecPROSPECT_FullRange"

data-raw/DATASET.R

@@ -6,5 +6,6 @@ ANT <- 2*runif(10)
 EWT <- 0.04*runif(10)
 LMA <- 0.02*runif(10)
 N <- 1+2*runif(10)
-Input_PROSPECT <- data.frame('CHL'=CHL,'CAR'=CAR,'ANT'=ANT,'EWT'=EWT,'LMA'=LMA,'N'=N)
+Input_PROSPECT <- data.frame('CHL'=CHL,'CAR'=CAR,'ANT'=ANT,
+                             'EWT'=EWT,'LMA'=LMA,'N'=N)
 

paper/paper.md

@@ -75,11 +75,14 @@ spectroscopy [@jay_physically-based_2016] and PROSAIL for canopy reflectance mod
 Note that PROSPECT is also available in packages written in [python](https://github.com/jgomezdans/prosail), 
 [Julia](https://github.com/RemoteSensingTools/CanopyOptics.jl) and [R](https://github.com/ashiklom/rrtm).
 
-The R package `prospect` includes recent versions of PROSPECT, and aims 
-at providing up-to-date developments in terms of model version and inversion strategies. 
+PROSPECT versions 4 and 5 developed by [@feret2008] are deprecated. 
+Therefore PROSPECT-D and PROSPECT-PRO are recommended versions. 
+The R package `prospect` includes recent versions of PROSPECT (D and PRO), 
+and aims at providing up-to-date developments in terms of future model version 
+and inversion strategies. 
 This includes parameterizable inversion routines, to ease physical model inversion 
 for beginners, and to help advanced users in designing and testing their own 
-inversion strategy.
+inversion strategy. 
 
 
 # Overview
@@ -116,6 +119,8 @@ LMA: leaf mass per area; PROT: proteins; CBC: carbon based constituents).\label{
 As PROSPECT is a relatively simple and computationally efficient model, 
 iterative optimization is the most widespread method to invert PROSPECT 
 and assess leaf chemistry and structure from their optical properties. 
+It usually takes less than 1 second to perform PROSPECT inversion, which is acceptable
+when processing experimental datasets of leaf optical properties including 100-1000 samples.
 Iterative optimization aims at minimizing a cost function comparing 
 measured and simulated leaf optical properties. 
 This procedure is based on the function `fmincon` included in the package `pracma`.
@@ -350,4 +355,4 @@ the initial version of the PROSPECT model.
 We also warmly thank Luc Bidel, Christophe François and Gabriel Pavan who 
 collected the ANGERS data set.
 
-# References
+# References

tests/testthat/test-Invert_PROSPECT.R

@@ -12,8 +12,10 @@ test_that("PROSPECT-D inversion produces accurate biophysical assessment", {
   expect_true(abs(leafBP$EWT-BPinit$EWT)<1e-6)
   expect_true(abs(leafBP$LMA-BPinit$LMA)<1e-6)
 
-  lrt$Reflectance <- lrt$Reflectance*(1+rnorm(length(lrt$Reflectance),0,0.01))
-  lrt$Transmittance <- lrt$Transmittance*(1+rnorm(length(lrt$Transmittance),0,0.01))
+  lrt$Reflectance <- lrt$Reflectance*(1+rnorm(length(lrt$Reflectance),
+                                              0,0.01))
+  lrt$Transmittance <- lrt$Transmittance*(1+rnorm(length(lrt$Transmittance),
+                                                  0,0.01))
 
   leafBP <- Invert_PROSPECT(Refl = lrt$Reflectance,
                             Tran = lrt$Transmittance)

tests/testthat/test-Invert_PROSPECT_OPT.R

@@ -12,12 +12,15 @@ test_that("PROSPECT-D inversion over optimal domains produces accurate biophysic
   expect_true(abs(leafBP$EWT-BPinit$EWT)<1e-7)
   expect_true(abs(leafBP$LMA-BPinit$LMA)<1e-7)
 
-  lrt$Reflectance <- lrt$Reflectance*(1+rnorm(length(lrt$Reflectance),0,0.01))
-  lrt$Transmittance <- lrt$Transmittance*(1+rnorm(length(lrt$Transmittance),0,0.01))
+  lrt$Reflectance <- lrt$Reflectance*(1+rnorm(length(lrt$Reflectance),
+                                              0,0.01))
+  lrt$Transmittance <- lrt$Transmittance*(1+rnorm(length(lrt$Transmittance),
+                                                  0,0.01))
   leafBPopt <- Invert_PROSPECT_OPT(lambda = lrt$wvl,
                                    Refl = lrt$Reflectance,
                                    Tran = lrt$Transmittance,
-                                   Parms2Estimate = c('CHL', 'CAR', 'EWT', 'LMA'))
+                                   Parms2Estimate = c('CHL', 'CAR',
+                                                      'EWT', 'LMA'))
   expect_true(abs(leafBPopt$CHL-BPinit$CHL)<1e-0)
   expect_true(abs(leafBPopt$CAR-BPinit$CAR)<1e-0)
   expect_true(abs(leafBPopt$EWT-BPinit$EWT)<1e-4)

vignettes/prospect1.Rmd

@@ -78,7 +78,7 @@ When run without input parameters, `PROSPECT` is run with default values:
 ```{r prospect direct mode default}
 library(prospect)
 LRT_default <- PROSPECT()
-# the following command is equivalent for simulation over the full spectral domain 
+# the following command is equivalent when simulating over the full spectral domain 
 LRT_default <- PROSPECT(SpecPROSPECT = prospect::SpecPROSPECT_FullRange)
 
 ```

vignettes/prospect2.Rmd

@@ -113,8 +113,8 @@ SubData <- FitSpectralData(lambda = LRT_D$wvl,
                            Tran = LRT_D$Transmittance,
                            UserDomain = SpectralSubDomain)
 
-# Note that FitSpectralData can also run with UserDomain defining upper and lower bounds 
-# Then you will need to set UL_Bounds = TRUE
+# Note that FitSpectralData can also run with UserDomain defining 
+# upper and lower bounds when setting input argument 'UL_Bounds = TRUE'
 ULBounds <- c(400,800)
 SubData <- FitSpectralData(lambda = LRT_D$wvl, 
                            Refl = LRT_D$Reflectance, 
@@ -189,7 +189,8 @@ Parms2Estimate  <- c('CHL','CAR','ANT','EWT','LMA')
 # define initial values for the inversion
 InitValues <- data.frame(CHL = 40, CAR = 8, ANT = 0.1, BROWN = 0, 
                          EWT = 0.01, LMA = 0.01, N = 1.5)
-# call Invert_PROSPECT_OPT in order to automaticall get optimal estimation of leaf parameters following latest published results
+# call Invert_PROSPECT_OPT to get optimal estimation of leaf parameters 
+# using optimal spectral domains
 ParmEst <- Invert_PROSPECT_OPT(lambda = LRT_D$wvl, 
                                Refl = LRT_D$Reflectance,
                                Tran = LRT_D$Transmittance,

vignettes/prospect3.Rmd

@@ -49,7 +49,7 @@ fileName <- list('DataBioch.txt','ReflectanceData.txt','TransmittanceData.txt')
 DataBioch <- fread(file.path(gitlab_Rep,dbName,fileName[[1]]))
 Refl <- fread(file.path(gitlab_Rep,dbName,fileName[[2]]))
 Tran <- fread(file.path(gitlab_Rep,dbName,fileName[[3]]))
-# Get the wavelengths corresponding to the reflectance and transmittance measurements  
+# Get wavelengths corresponding to the reflectance & transmittance measurements  
 lambda <- Refl$wavelength
 Refl$wavelength <- NULL
 Tran$wavelength <- NULL
@@ -69,7 +69,7 @@ Experimental leaf optics and optical constants of PROSPECT need to be adjusted b
 Parms2Estimate  <- 'ALL'
 InitValues <- data.frame(CHL = 40, CAR = 10, ANT = 0.1, BROWN = 0, 
                          EWT = 0.01, LMA = 0.01, N = 1.5)
-# adjust PROSPECT optical constants and experimental leaf optics before inversion
+# adjust PROSPECT optical constants & experimental leaf optics before inversion
 SubData <- FitSpectralData(lambda = lambda,
                            Refl = Refl, 
                            Tran = Tran)