#' computes NMDS # #' @param MatBCdist BC dissimilarity matrix #' @param dimMDS numeric. number of dimensions of the NMDS # #' @return BetaNMDS_sel #' @importFrom future plan multisession sequential #' @importFrom future.apply future_lapply #' @importFrom ecodist nmds #' @importFrom utils find #' @export

Source: R/Lib_MapBetaDiversity.R

compute_NMDS <- function(MatBCdist,dimMDS=3) nbiterNMDS <- 4 if (Sys.info()["sysname"] == "Windows") nbCoresNMDS <- 2 else if (Sys.info()["sysname"] == "Linux") nbCoresNMDS <- 4 # multiprocess of spectral species distribution and alpha diversity metrics # plan(multisession, workers = nbCoresNMDS) ## Parallelize using four cores plan(multisession, workers = nbCoresNMDS) ## Parallelize using four cores BetaNMDS <- future_lapply(MatBCdist, FUN = nmds, mindim = dimMDS, maxdim = dimMDS, nits = 1, future.packages = c("ecodist")) plan(sequential) # find iteration with minimum stress Stress <- vector(length = nbiterNMDS) for (i in 1:nbiterNMDS) Stress[i] <- BetaNMDS[[i]]$stress print("Stress obtained for NMDS iterations:") print(Stress) print("Rule of thumb") print("stress < 0.05 provides an excellent represention in reduced dimensions") print("stress < 0.1 is great") print("stress < 0.2 is good") print("stress > 0.3 provides a poor representation") MinStress <- find(Stress == min(Stress)) BetaNMDS_sel <- BetaNMDS[[MinStress]]$conf BetaNMDS_sel <- data.frame(BetaNMDS_sel[[1]]) return(BetaNMDS_sel) Identifies ordination coordinates based on nearest neighbors

ordination_to_NN(
  SSD_subset,
  Beta_Ordination_sel,
  Sample_Sel,
  nb_partitions,
  nbclusters,
  pcelim = 0.02,
  nbCPU = 1,
  SamplesPerThread = 2000,
  progressbar = FALSE
)

Arguments

SSD_subset

numeric. matrix corresponding to Spectral species distribution for a set of windows

Beta_Ordination_sel

ordination of dissimilarity matrix for a selection of spatial units

Sample_Sel

numeric. Samples selected during ordination

nb_partitions

number of k-means then averaged

nbclusters

number of clusters

pcelim

numeric. Minimum contribution in percent required for a spectral species

nbCPU

numeric. number of CPUs available

SamplesPerThread

numeric. number of samples to be processed per thread for dissimilarity matrix

progressbar

boolean. should progress bar be displayed (set to TRUE only if no conflict of parallel process)

Value

Ordination_est coordinates of each spatial unit in ordination space