add R script

FungusNameCheck.R

@@ -0,0 +1,75 @@
+#!/usr/bin/env Rscript
+##Script to check a list of fungal species names for the most up to date classification in Index Fungorum##
+
+message("\n-----------------------")
+message("FungusNameCheck.R")
+message("PID:", Sys.getpid())
+message(Sys.time())
+message("-----------------------\n")
+
+args <- commandArgs(trailingOnly=TRUE)
+
+#Test if the correct packages are installed
+if (require(taxize) == FALSE) {
+  stop("Please install the taxize package!", call.=FALSE)
+} 
+
+#Test if there is one argument: if not, return an error
+if (length(args) != 1) {
+  stop("\nOne argument must be supplied: input file containing a list of fungi species names with no header", call.=FALSE)
+} 
+
+list <- args[1]
+
+#Read in species datasheet
+species.df <- read.csv(list, header=FALSE)
+#Remove whitespace
+species.df$V1 <- trimws(species.df$V1)
+
+message("\nCross-checking list of ", length(species.df$V1), " fungi from ", list, "\n")
+
+#Make dataframe to collect results checking current names (replace with your own species dataframe/the combined tree dataframe)
+species.check.df <- data.frame(input_name=unique(species.df$V1),
+                               IF_current_name=NA)
+
+#####INDEX FUNGORUM NAME CHECKING LOOP#######
+#Write for loop to run the name check on each species
+pb <- txtProgressBar(min=0, max=length(species.check.df$input_name), initial=0, style=3) 
+
+for (i in 1:length(species.check.df$input_name)) { 
+
+  setTxtProgressBar(pb, i)
+  result <- fg_name_search(species.check.df$input_name[i])
+
+  #Check for successful search result
+  if (length(result) > 0) {
+
+    #Check for 'current name' column
+    if ("current_name" %in% colnames(result)) {
+
+      #Check for the first hit that is exact and has a 'current name'
+      for (j in 1:length(result$name_of_fungus)) {
+
+        if (result$name_of_fungus[j] == species.check.df$input_name[i] &
+            !is.na(result$current_name[j]) &
+            is.na(species.check.df$IF_current_name[i])) {
+
+          species.check.df$IF_current_name[i] <- result$current_name[j]
+        }  
+
+        #Stop checking once the current name is found
+        if (!is.na(species.check.df$IF_current_name[i])) break
+
+      }
+
+      #If no current name column (i.e. a single hit), check that the name hit is exact
+    } else if (result$name_of_fungus[1] == species.check.df$input_name[i])
+
+      species.check.df$IF_current_name[i] <- result$name_of_fungus[1]
+  }
+}
+
+#Write results to file
+write.csv(species.check.df, paste0("checked_names_PID", Sys.getpid(), ".csv"), row.names=FALSE, quote=FALSE)
+
+message("Results saved in checked_names_PID", Sys.getpid(), ".csv")