Mercurial > repos > ecology > ecoregion_clara_cluster

annotate GeoNN.R @ 2:a7269e5eed27 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
author ecology
date Wed, 28 May 2025 10:11:06 +0000
parents 88964fcccfef
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88964fcccfef planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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1 #Date : 09/02/2024
88964fcccfef planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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2 #Author : Seguineau Pauline
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88964fcccfef planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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4 #Load libraries
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5 library(tidyr)
88964fcccfef planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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6 library(dplyr)
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7 library(sf)
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9 #load arguments
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10 args = commandArgs(trailingOnly=TRUE)
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11 if (length(args)==0)
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12 {
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13 stop("This tool needs at least one argument")
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14 }else{
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15 enviro <- args[1]
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16 envlong <- as.numeric(args[2])
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17 envlat <- as.numeric(args[3])
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18 occu <- args[4]
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19 occulat <- as.numeric(args[5])
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20 occulong <- as.numeric(args[6])
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21 }
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23 env = read.table(enviro, header = TRUE, sep="\t")
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24 occ = read.table(occu, header = TRUE, sep = "\t")
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26 cols_env = c(names(env[envlong]),names(env[envlat]))
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27 cols_occ = c(names(occ[occulong]),names(occ[occulat]))
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29 ###calculate distances###
88964fcccfef planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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30 #transform tables into sf object
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32 env_sf <- st_as_sf(env, coords = cols_env, crs = "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
88964fcccfef planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit e03df85746a3b61a382a5ee7e3357a8bf42a5097
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33 occ_sf <- st_as_sf(occ, coords = cols_occ, crs = "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
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35 #Find the indices of env_sf entities closest to each point in occ_sf.
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37 nearest_indices <- st_nearest_feature(occ_sf, env_sf)
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39 nearest_points <- env[nearest_indices, ]
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41 # Calculate distances between env_sf and occ_sf points
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42 distances <- st_distance(env_sf, occ_sf)
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44 #Extract the corresponding distances between occ and env
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46 nearest_distances <- numeric(length(nearest_indices))
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48 for (i in 1:length(nearest_indices)) {
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49 nearest_distances[i] <- st_distance(env_sf[nearest_indices[i],], occ_sf[i,])
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50 }
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52 #assemble occurrences and environmental parameters in the same file
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54 nearest_points <- nearest_points[, !names(nearest_points) %in% cols_env] #remove lat and long from env to clean data
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55 new_occ = cbind(occ, nearest_points)
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57 #Save the file
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59 write.table(new_occ, file = "occurrence_env.tsv",sep ="\t",quote = F, row.names = F,col.names = T)
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61 #create an information file with the distances between the points of the two files
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63 distance_info <- data.frame(
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64 occ_geometry = occ_sf$geometry,
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65 env_geometry = env_sf$geometry[nearest_indices],
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66 distance = nearest_distances
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67 )
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69 colnames(distance_info)[1] <- "occ_geometry"
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70 colnames(distance_info)[2] <- "env_geometry"
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71 colnames(distance_info)[3] <- "Distances (meters)"
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72 #save the information file
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74 write.table(distance_info, file = "infos_file.tsv",sep ="\t",quote = F, row.names = F,col.names = T)
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