Mercurial > repos > ecology > estimate_endem

annotate EstimEndem.R @ 1:f3a977826375 draft default tip

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author ecology
date Thu, 05 Jun 2025 16:50:45 +0000
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1 #!/bin/Rscript
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2 # phyloregions
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4 args = commandArgs(trailingOnly=TRUE)
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5 #args = c("input/matrix_file", "input/tree_file.txt", "input/grid_aq_3_PF.shp")
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7 # library
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8 library(phyloregion)
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9 library(ape)
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10 library(Matrix)
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11 library(SparseArray)
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12 library(sf)
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13 library(sp)
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14 library(raster)
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15 library(dplyr)
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18 save_sf <- function(){
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19 #st_write(phyloreg_sf[,-(3:5)], paste0(tempdir(), "/", "output.shp"), delete_layer = TRUE)
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20 write_sf(phyloreg_sf, "output.shp")
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21 }
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24 if (length(args)<5){stop('Usage : sparseMatrix.csv tree.txt grid.shp nb_clust clust_method')
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25 }else{
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26 # read enter files
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27 comm_tree <- read.tree(args[1])
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29 comm_matrix <- readSparseCSV(args[2], sep = "\t")
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30 comm_matrix <- as(comm_matrix,"dgCMatrix")
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32 grid <- read_sf(args[3])
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34 nb_clust <- as.integer(args[4])
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36 clust_method <- toString(args[5])
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f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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38 # calculate phylogenetic Beta diversity - a phylogenetic distance matrix between grid cells
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39 phylo_beta <- phylobeta(comm_matrix, comm_tree, index.family = "sorensen")
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41 #select the less distorting clustering method, best fitting between phylogenetic distances in phylobeta matrix
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42 # and raw distances from branch lengths of the tree
f7a55ccf2a3e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Phylodiversity_workflow commit 0de557d919c26eb0b5ab61504bc597d551503ac3
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43 select_linkage(phylo_beta[[1]])
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45 #select optimal number of clusters with selected method
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46 optim <- optimal_phyloregion(phylo_beta[[3]])
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47 print(paste("the best number of cluster is :", optim$optimal$k))
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48 #plot(optim$df$k, optim$df$ev, pch = 20) # k - nbr of clusters VS explained variance given k
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49 # k has to be selected by a user
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51 # pass the grid cell to spatial format
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52 grid_sp <- as_Spatial(grid)
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53 #proj4string(grid_sp)
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55 # calculate phyloregions clusters
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56 y <- phyloregion(phylo_beta[[3]], pol = grid_sp, k = nb_clust, method = clust_method)
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57 #summary(y)
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58 #phylo_nmds <- y$NMDS
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60 # take an shp spatial file for phyloregions and put it to sf format
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61 phyloreg_sf <- y$pol
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62 # print(st_crs(phyloreg_sf))
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63 #plot(phyloreg_sf)
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64 phyloreg_sf <- st_as_sf(phyloreg_sf, crs = st_crs(grid))
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65 # print(st_crs(phyloreg_sf))
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67 names(phyloreg_sf)[3:8] <- c("R_val", "G_val", "B_val", "r_code", "g_code", "b_code")
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70 save_sf()
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71 }
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74 # sf_recup <- read_sf("output.shp")
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