--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PhylOccuMatcher.R	Tue May 20 09:53:38 2025 +0000
@@ -0,0 +1,48 @@
+#!/bin/Rscript
+# Matice Phylo/Commu
+
+args = commandArgs(trailingOnly=TRUE)
+#args = c( "pycnogonida_tree_2024", "pycnogonida_occ_2024.csv")
+
+library(phyloregion)
+library(ape)
+library(Matrix)
+library(SparseArray)
+
+#install.packages("remotes")
+#remotes::install_github("Bioconductor/SparseArray")
+
+save_as_tabular_fun <- function(){
+  #writeMM(obj = comm_matrix, file = "output.mtx")
+  writeSparseCSV(comm_matrix, out_grid, sep="\t", transpose=FALSE, write.zeros=FALSE)
+}
+
+
+save_as_tree_fun <- function(){
+  write.tree(comm_tree, file = out_tree)
+}
+
+
+if (length(args)<4){stop('Usage : input_tree_file input_grid_file output_tree_file output_grid_file')
+}else{
+  tree <- read.tree(args[1])
+  grid <- read.csv2(args[2], dec = ".", sep = "\t", header = T, na.strings = "")
+  out_tree <- args[3]
+  out_grid <- args[4]
+  
+  sparse_grid <- long2sparse(grid, grid = "grids", species = "newscientificname")
+  
+  com.data <- match_phylo_comm(tree, sparse_grid, delete_empty_rows = F)
+  
+  comm_matrix <- com.data$comm
+  #test
+  #sum_matrix <- summary(comm_matrix)
+  
+  comm_tree <- com.data$phy
+
+  save_as_tabular_fun()
+  save_as_tree_fun()
+}
+
+#comm_matrix_recup <- readSparseCSV("output")
+#comm_matrix_recup <- as(comm_matrix_recup,"dgCMatrix")