minor update

- update CI
- update news
- update paper

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,32 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@v1
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes", "rcmdcheck"))
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+      - name: Check
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
+        shell: Rscript {0}

.gitlab-ci.yml

@@ -26,7 +26,6 @@ before_script:
 stages:
 - deps
 - check
-- test
 - deploy
 
 deps:
@@ -46,24 +45,6 @@ check:
     - master
     - schedules
 
-test:
-  stage: test
-  script:
-  - R -e "devtools::install_deps(dependencies = TRUE)"
-  - R CMD build . --no-build-vignettes --no-manual
-  - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
-  - R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual
-  cache:
-    key: "$CI_COMMIT_REF_SLUG"
-    paths:
-      - installed_deps/
-  artifacts:
-  paths:
-    - '*.Rcheck/'
-  only:
-    - master
-
-
 pages:
   stage: deploy
   script:

NEWS.md

@@ -10,6 +10,7 @@ version following reviews for publication in JOSS
 - add CONTRIBUTION.md and CODE_OF_CONDUCT.md (Issue#8: Add contribution guide)
 - update documentation and harmonize with corresponding code for JOSS manuscript (Issue#10: harmonize web tutorial with JOSS manuscript examples)
 - overall update of the code to work with dataframes more systematically
+- only two versions now defined in the package (D and PRO), and the use of brown pigments is accessible during inversion by setting Est_Brown_Pigments == TRUE
 
 ## fixes
 - fixed error occuring when PROSPECT-PRO inversion performed to assess EWT

paper/paper.md

@@ -164,7 +164,8 @@ They are accessible through the variable `SpecPROSPECT_FullRange`, a data frame
 which is automatically loaded with the package. 
 Multiple functions in the package `prospect` expect a variable `SpecPROSPECT` as input. 
 `SpecPROSPECT_FullRange` is used as default value when this input variable is not defined. 
-Users can create a new variable and modify the spectral domain from `SpecPROSPECT_FullRange`. 
+Users can adjust `SpecPROSPECT_FullRange` in order to adjust the spectral characteristics 
+for simulation, including spectral domain, sampling or sensor-specicif spectral response. 
 
 These two examples illustrate how to run PROSPECT. 
 The function `PROSPECT` identifies the version to be used: PROSPECT-D is used 
@@ -246,10 +247,9 @@ library(data.table)
 # download ANGERS leaf optics database from gitlab repository
 gitlab_Rep <- 'https://gitlab.com/jbferet/myshareddata/raw/master/LOP'
 # download leaf biochemical constituents and leaf optical properties
-fileName <- list('DataBioch.txt','ReflectanceData.txt','TransmittanceData.txt')
-DataBioch <- data.table::fread(file.path(gitlab_Rep,'ANGERS',fileName[[1]]))
-Refl<- data.table::fread(file.path(gitlab_Rep,'ANGERS',fileName[[2]]))
-Tran <- data.table::fread(file.path(gitlab_Rep,'ANGERS',fileName[[3]]))
+DataBioch <- data.table::fread(file.path(gitlab_Rep,'ANGERS/DataBioch.txt'))
+Refl<- data.table::fread(file.path(gitlab_Rep,'ANGERS/ReflectanceData.txt'))
+Tran <- data.table::fread(file.path(gitlab_Rep,'ANGERS/TransmittanceData.txt'))
 # Get the wavelengths corresponding to reflectance and transmittance measurements  
 lambda <- Refl$wavelength
 Refl$wavelength <- Tran$wavelength <- NULL
@@ -285,7 +285,7 @@ This list of parameters is defined with the variable `Parms2Estimate`.
 The default parameterization of PROSPECT inversion assesses all parmeters 
 listed in Table \ref{table:1} except BROWN, which can be assessed by setting 
 `Est_Brown_Pigments = TRUE` as input for `Invert_PROSPECT`.
-The value set for parameters which are not estimated is then defined with 
+The value set for parameters which are not assessed is then defined with 
 the `InitValues` input variable. 
 
 ```r
@@ -329,6 +329,11 @@ constituent content either from directional-hemispherical reflectance and
 transmittance, or from reflectance or transmittance only. 
 `prospect` provides latest advances in terms of model version and inversion 
 procedures to the leaf spectroscopy community. 
+`prospect` is coupled with the canopy model SAIL through the R package [`prosail`](https://jbferet.gitlab.io/prosail/index.html).
+`prosail` is dedicated to applications focusing on Earth observation imagery analysis 
+and allows simulation of canopy reflectance for multispectral and hyperspectral sensors.
+Hybrid inversions based on physical modeling and machine learning are also implemented 
+in `prosail` to assess vegetation traits from imagery data.
 
 
 # Availability
@@ -347,3 +352,4 @@ We also warmly thank Luc Bidel, Christophe François and Gabriel Pavan who
 collected the ANGERS data set.
 
 # References
+0