diff GeoNN.R @ 2:24a81631a8b5 draft

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GeoNN.R	Thu Mar 21 14:04:36 2024 +0000
@@ -0,0 +1,77 @@
+#Date : 09/02/2024
+#Author : Seguineau Pauline
+
+#Load libraries
+library(tidyr)
+library(dplyr)
+library(sf)
+
+#load arguments
+args = commandArgs(trailingOnly=TRUE) 
+if (length(args)==0)
+{
+    stop("This tool needs at least one argument")
+}else{
+    enviro <- args[1]
+    envlong <- as.numeric(args[2])
+    envlat <- as.numeric(args[3])
+    occu <- args[4]
+    occulat <- as.numeric(args[5])
+    occulong <- as.numeric(args[6])
+}
+ 
+env = read.table(enviro, header = TRUE, sep="\t")
+occ = read.table(occu, header = TRUE, sep = "\t")
+
+cols_env = c(names(env[envlong]),names(env[envlat]))
+cols_occ = c(names(occ[occulong]),names(occ[occulat]))
+
+###calculate distances### 
+#transform tables into sf object
+
+env_sf <- st_as_sf(env, coords = cols_env, crs = "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
+occ_sf <- st_as_sf(occ, coords = cols_occ, crs = "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
+
+#Find the indices of env_sf entities closest to each point in occ_sf.
+
+nearest_indices <- st_nearest_feature(occ_sf, env_sf)
+
+nearest_points <- env[nearest_indices, ]
+
+# Calculate distances between env_sf and occ_sf points
+distances <- st_distance(env_sf, occ_sf)
+
+#Extract the corresponding distances between occ and env
+
+nearest_distances <- numeric(length(nearest_indices))
+
+for (i in 1:length(nearest_indices)) {
+  nearest_distances[i] <- st_distance(env_sf[nearest_indices[i],], occ_sf[i,])
+}
+
+#assemble occurrences and environmental parameters in the same file
+
+nearest_points <- nearest_points[, !names(nearest_points) %in% cols_env] #remove lat and long from env to clean data
+new_occ = cbind(occ, nearest_points)
+
+#Save the file 
+
+write.table(new_occ, file = "occurrence_env.tsv",sep ="\t",quote = F, row.names = F,col.names = T)
+
+#create an information file with the distances between the points of the two files 
+
+distance_info <- data.frame(
+  occ_geometry = occ_sf$geometry,
+  env_geometry = env_sf$geometry[nearest_indices],
+  distance = nearest_distances
+)
+
+colnames(distance_info)[1] <- "occ_geometry"
+colnames(distance_info)[2] <- "env_geometry"
+colnames(distance_info)[3] <- "Distances (meters)"
+#save the information file
+
+write.table(distance_info, file = "infos_file.tsv",sep ="\t",quote = F, row.names = F,col.names = T)
+
+
+