--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/indval.R	Wed Jul 23 14:36:07 2025 +0000
@@ -0,0 +1,59 @@
+#Seguineau Pauline
+#02/12/2024
+#Indicspecies tool
+
+library(dplyr)
+library(indicspecies)
+
+#load arguments
+args = commandArgs(trailingOnly=TRUE) 
+if (length(args)==0)
+{
+    stop("This tool needs at least one argument")
+}else{
+    clus_pts <- args[1]
+    occ <- args[2]
+    spe_name <- args[3]
+    sign <- args[4]
+}
+
+###load data
+clus <- read.table(clus_pts, dec=".", sep="\t", header=T,na.strings = "na") #cluster points file (ecoregionalization workflow)
+data.col <- read.table(occ, dec=".", sep="\t", header=T,na.strings = "na") #occurrence file (merged table from ecoregionalization workflow)
+spe_name = strsplit(spe_name, ",")
+spname=NULL
+
+for (n in spe_name) {
+spname = cbind(names(data.col[as.numeric(n)]))}
+
+#Rename decimalLatitude and decimalLongitude columns from occurrence file
+if ("decimalLatitude" %in% colnames(data.col)) {
+   colnames(data.col)[which(colnames(data.col) == "decimalLatitude")] <- "lat"
+}
+if ("decimalLongitude" %in% colnames(data.col)) {
+   colnames(data.col)[which(colnames(data.col) == "decimalLongitude")] <- "long"
+}
+
+#Round lat and long of the data.col file to be able to put clus cluster in it
+data.col$lat = round(data.col$lat,digits = 2)
+data.col$long = round(data.col$long,digits = 2)
+
+# Creates a new "station" column that associates a unique identifier to each latitude-longitude pair
+data.col <- data.col %>% mutate(station = as.factor(paste(lat, long, sep = "_")))
+
+# convert "station" to a unique numeric identifier
+data.col <- data.col %>%  mutate(station = as.numeric(factor(station)))
+
+#Adding clusters to file
+clusta <- merge(data.col,clus, by=c("lat","long"), all.x = TRUE)
+
+#This generated duplicates with different clusters
+clusta <- aggregate(clusta, by=list(clusta$station,clusta$cluster), FUN=mean, na.rm=TRUE)
+clusta <- na.exclude(clusta)
+
+# indval on all clusters
+indval = multipatt(clusta[,spname], clusta$cluster,duleg = TRUE, control = how(nperm=999))
+if (sign=="true"){
+	capture.output(summary(indval,indvalcomp=TRUE), file = "indval.txt")
+}else{
+	capture.output(summary(indval,indvalcomp=TRUE, alpha=1), file = "indval.txt")}