# biodivMapR2 v2.2.0

## change - merge v2 from gitlab repository - update vignettes for use of v2
jbferet · Jan 24, 2025 · cb93ca6 · cb93ca6
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,6 +1,7 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^doc
+^doc/
 ^examples
 ^TODO.md
 ^\.travis\.yml$

diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,5 @@
 Meta
-doc
+doc/
 .Rproj.user
 .Rbuildignore
 .Rhistory

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: biodivMapR
 Title: biodivMapR: an R package for a- and ß-diversity mapping using remotely-sensed images
-Version: 2.1.4
+Version: 2.2.0
 Authors@R: c(person(given = "Jean-Baptiste", 
 					family = "Feret", 
 					email = "[email protected]", 
@@ -13,27 +13,24 @@ Authors@R: c(person(given = "Jean-Baptiste",
 					comment = c(ORCID = "0000-0002-2185-9952", "clean code, format as package, build website")))
 Description: this packages allows processing image data based on the method described in the following publication:
     Féret, J.-B., Asner, G.P., 2014. Mapping tropical forest canopy diversity using high-fidelity imaging spectroscopy. Ecol. Appl. 24, 1289–1296. https://doi.org/10.1890/13-1824.1
-    It expects a raster file as input, with ENVI HDR header file including spectral bands of the sensor, if optical sensor.
+    biodivMapR v2 produces spectral diversity maps, and more broadly 'remotely sensed' diversity maps. 
+    It can process any type of raster data, as long as the driver is compatible with drivers accepted by the terra package. 
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 License: GPL-3 + file LICENSE
 LazyData: true
 Imports: 
-    ape,
     bigRaster,
     cli,
     dissUtils,
     doFuture,
-    doParallel,
     dplyr,
     fields,
     foreach,
+    fundiversity,
     future,
     future.apply,
-    geometry,
-    labdsv,
-    pracma,
     progress,
     progressr,
     purrr,
@@ -43,11 +40,13 @@ Imports:
     stats,
     terra,
     tidyr,
-    tools,
-    vegan,
-    zip
+    vegan
 Suggests: 
+    ggplot2, 
+    gridExtra, 
     knitr,
+    RColorBrewer, 
+    readr,
     rmarkdown,
     testthat (>= 2.0.0)
 Remotes: gitlab::jbferet/bigRaster

diff --git a/NAMESPACE b/NAMESPACE
@@ -43,40 +43,44 @@ export(get_image_bands)
 export(get_kmeans)
 export(get_raster_diversity)
 export(get_raster_extent)
-export(get_raster_functional)
 export(get_spectralSpecies)
 export(get_sunlitwindows)
 export(get_xy_samples)
 export(init_PCoA)
+export(init_PCoA_samples)
 export(init_kmeans)
+export(init_kmeans_samples)
 export(kmeans_iter)
 export(kmeans_progressr)
-export(load_tutorialdataset)
 export(maxRows_chunk)
+export(mnf)
 export(nbRows_chunk)
+export(noise)
 export(pca)
+export(pco)
 export(perform_PCA)
 export(print_error_message)
 export(produce_win_ID)
 export(radiometric_filtering)
 export(radiometricfilter_chunk)
+export(randperm)
 export(read_ENVI_header)
 export(repmat)
 export(rm_invariant_bands)
 export(sample_exact_raster)
 export(sample_from_raster)
+export(sample_from_raster_coords)
 export(sample_plots_from_raster)
 export(sample_raster)
 export(save_diversity_maps)
+export(scatter_alphabeta)
 export(select_PCA_components)
 export(spectralspecies_per_polygon)
 export(split_chunk)
 export(split_line)
 export(wrapperBig_PCA)
 import(cli)
-import(doParallel)
 import(tools)
-importFrom(ape,mst)
 importFrom(bigRaster,apply_bigRaster)
 importFrom(dissUtils,diss)
 importFrom(doFuture,registerDoFuture)
@@ -91,15 +95,17 @@ importFrom(dplyr,select)
 importFrom(fields,rdist)
 importFrom(foreach,"%dopar%")
 importFrom(foreach,foreach)
+importFrom(fundiversity,fd_fdis)
+importFrom(fundiversity,fd_fdiv)
+importFrom(fundiversity,fd_feve)
+importFrom(fundiversity,fd_fric)
+importFrom(fundiversity,fd_raoq)
 importFrom(future,multisession)
 importFrom(future,plan)
 importFrom(future,sequential)
 importFrom(future.apply,future_lapply)
-importFrom(geometry,convhulln)
-importFrom(labdsv,pco)
 importFrom(parallel,makeCluster)
 importFrom(parallel,stopCluster)
-importFrom(pracma,randperm)
 importFrom(progress,progress_bar)
 importFrom(progressr,handlers)
 importFrom(progressr,progressor)
@@ -111,8 +117,9 @@ importFrom(sf,st_sample)
 importFrom(snow,splitRows)
 importFrom(stats,IQR)
 importFrom(stats,as.dist)
+importFrom(stats,cmdscale)
 importFrom(stats,cor.test)
-importFrom(stats,dist)
+importFrom(stats,cov)
 importFrom(stats,kmeans)
 importFrom(stats,na.omit)
 importFrom(stats,prcomp)
@@ -142,9 +149,7 @@ importFrom(terra,xyFromCell)
 importFrom(tidyr,nest)
 importFrom(tidyr,unnest)
 importFrom(tools,file_path_sans_ext)
-importFrom(utils,download.file)
 importFrom(utils,file.edit)
 importFrom(utils,read.csv)
 importFrom(vegan,fisher.alpha)
 importFrom(vegan,mantel)
-importFrom(zip,unzip)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# biodivMapR2 v2.2.0
+## change
+- merge v2 from gitlab repository
+- update vignettes for use of v2 
+
 # biodivMapR2 v2.1.4
 ## fix
 - in 'get_diversity_from_plots' : 

diff --git a/R/apply_continuum_removal.R b/R/apply_continuum_removal.R
@@ -5,9 +5,6 @@
 #
 #' @return samples from image and updated number of pixels to sample if necessary
 #' @importFrom snow splitRows
-#' @importFrom future plan multisession sequential
-#' @importFrom future.apply future_lapply
-#' @importFrom progressr progressor handlers with_progress
 #' @export
 
 apply_continuum_removal <- function(Spectral_Data, Spectral) {

diff --git a/R/biodivMapR_OptClusters.R b/R/biodivMapR_OptClusters.R
@@ -22,11 +22,9 @@
 #'
 #' @return list including performances (correlation) of SFS with additional
 #' features and assessed diversity metrics corresponding to each step
-#' @import doParallel
 #' @importFrom doFuture registerDoFuture
 #' @importFrom future plan multisession sequential
 #' @importFrom foreach foreach %dopar%
-#' @importFrom dplyr group_split
 #' @importFrom vegan mantel
 #' @importFrom progress progress_bar
 #' @importFrom stats cor.test
@@ -98,6 +96,7 @@ biodivMapR_OptClusters <- function(input_raster, obs_vect, obs2optimize, SelectB
     registerDoFuture()
     cl <- parallel::makeCluster(nbCPU)
     plan("cluster", workers = cl)
+	kmit <- NULL
     get_diversity_from_plots_list <- function() {
       foreach(kmit = Kmeans_info) %dopar% {
         divplots <- get_diversity_from_plots(input_rast = input_raster,

diff --git a/R/biodivMapR_SFS.R b/R/biodivMapR_SFS.R
@@ -20,7 +20,6 @@
 #'
 #' @return list including performances (correlation) of SFS with additional
 #' features and assessed diversity metrics corresponding to each step
-#' @import doParallel
 #' @importFrom doFuture registerDoFuture
 #' @importFrom future plan multisession sequential
 #' @importFrom foreach foreach %dopar%
@@ -135,6 +134,7 @@ biodivMapR_SFS <- function(input_raster, obs_vect, obs2optimize,
 
   for (nbvars2select in seq_len(NbPCs_To_Keep)){
     NumVar_list <- as.list(seq_len(length(AllVars)))
+	numvar <- win_ID <- NULL
     subfeatures_SFS <- function() {
       foreach(numvar = NumVar_list) %dopar% {
         CorrVal <- Assess <- list()

diff --git a/R/biodivMapR_chunk.R b/R/biodivMapR_chunk.R
@@ -89,11 +89,13 @@ biodivMapR_chunk <- function(blk, r_in, window_size, Kmeans_info, Beta_info = NU
                                                         alphametrics = alphametrics,
                                                         Beta_info = Beta_info,
                                                         Hill_order = Hill_order,
-                                                        pcelim = pcelim)
+                                                        pcelim = pcelim, 
+														future.seed = TRUE)
         if (!is.null(FDmetric)){
           FunctionalIdx_CPU <- future.apply::future_lapply(X = windows_per_CPU$SSwindow_perCPU,
                                                            FUN = functional_window_list,
-                                                           FDmetric = FDmetric)
+                                                           FDmetric = FDmetric, 
+                                                           future.seed = TRUE)
         }
         parallel::stopCluster(cl)
         plan(sequential)

diff --git a/R/explore_kmeans.R b/R/explore_kmeans.R
@@ -13,6 +13,7 @@
 #'
 #' @return Kmeans_info
 #' @importFrom dplyr select all_of
+#' @importFrom doFuture registerDoFuture
 #' @export
 
 explore_kmeans <- function(input_rast,
@@ -43,7 +44,7 @@ explore_kmeans <- function(input_rast,
   registerDoFuture()
   cl <- parallel::makeCluster(nbCPU)
   plan("cluster", workers = cl)
-
+  nbclust <- NULL
   get_kmeans_list <- function() {
     foreach(nbclust = nbClust_list) %dopar% {
       Kmeans_info <- get_kmeans(rast_sample = rast_sample,

diff --git a/R/get_diversity_from_plots.R b/R/get_diversity_from_plots.R
@@ -19,6 +19,7 @@
 #'
 #' @return SpatVector including diversity metrics and BC dissimilarity for the plots
 #' @importFrom dplyr group_split
+#' @importFrom stats as.dist
 #' @export
 
 get_diversity_from_plots <- function(input_rast, validation_vect,
@@ -31,7 +32,7 @@ get_diversity_from_plots <- function(input_rast, validation_vect,
                                      MinSun = 0.25, pcelim = 0.02, nbCPU = 1, getBeta = T,
                                      verbose = F){
   if (verbose == T) message('Compute diversity from vector plot network')
-  FunctDiv <- MatBC_Full <- NULL
+  FunctDiv <- MatBC_Full <- win_ID <- NULL
   # get nbIter and nbclusters
   nbIter <- length(Kmeans_info$Centroids)
   nbclusters <- dim(Kmeans_info$Centroids[[1]])[1]
@@ -169,7 +170,7 @@ get_diversity_from_plots <- function(input_rast, validation_vect,
     MatBC_Full[IDwindow,IDwindow] <- MatBC
     MatBCdist <- stats::as.dist(MatBC, diag = FALSE, upper = FALSE)
     colnames(MatBC_Full) <- rownames(MatBC_Full) <- Attributes$ID_biodivMapR
-    BetaPCO <- labdsv::pco(MatBCdist, k = dimPCO)
+    BetaPCO <- pco(MatBCdist, k = dimPCO)
     PCoA_BC <- matrix(data = NA,nrow = nbPlots_init, ncol = dimPCO)
     PCoA_BC[IDwindow,] <- BetaPCO$points
     Attributes$BetaPlots_PCoA_1 <- PCoA_BC[,1]

diff --git a/R/get_raster_functional.R b/R/get_raster_functional.R
diff --git a/R/get_sunlitwindows.R b/R/get_sunlitwindows.R
@@ -11,6 +11,7 @@
 #' @export
 #'
 get_sunlitwindows <- function(inputdata, pixperplot, MinSun = 0.25){
+  win_ID <- data <- ID <- NULL
   inputwindow <- inputdata %>% dplyr::group_by(win_ID) %>% nest()
   nbPix_Sunlit <- unlist(purrr::map(inputwindow$data,nrow))
   PCsun <- nbPix_Sunlit/pixperplot

diff --git a/R/get_xy_samples.R b/R/get_xy_samples.R
@@ -5,7 +5,6 @@
 #' @param input_mask SpatRaster. mask corresponding to raster to extract data from
 #'
 #' @return xy matrix
-#' @importFrom pracma randperm
 #' @importFrom terra values xyFromCell
 #' @export
 
@@ -17,7 +16,7 @@ get_xy_samples <- function(input_rast, nbSamples, input_mask = NULL){
   # adjust if mask provided
   if (!is.null(input_mask)) nbPixels <- sum(terra::values(input_mask),na.rm = T)
   if (nbSamples>nbPixels) nbSamples <- nbPixels
-  choicePix <- pracma::randperm(seq_len(nbPixels),nbSamples)
+  choicePix <- randperm(seq_len(nbPixels),nbSamples)
   if (!is.null(input_mask)){
     whichPix <- which(terra::values(input_mask)==1)
   } else {

diff --git a/R/init_PCoA.R b/R/init_PCoA.R
@@ -20,9 +20,6 @@
 #' @importFrom future plan multisession sequential
 #' @importFrom future.apply future_lapply
 #' @importFrom progressr progressor handlers with_progress
-#' @importFrom labdsv pco
-#' @importFrom dplyr group_split
-#' @importFrom stats as.dist
 #' @importFrom parallel makeCluster stopCluster
 #' @export