#!/usr/bin/env Rscript #library('getopt') #library(devtools) args = commandArgs(trailingOnly=TRUE) source(args[1]) #TODO replace by library(regionalGAM) if available as official package from bioconda tryCatch({input = read.table(args[2], header=TRUE,sep=" ")},finally={input = read.table(args[2], header=TRUE,sep=",")}) dataset1 <- input[,c("SPECIES","SITE","YEAR","MONTH","DAY","COUNT")] pheno <- flight_curve(dataset1) write.table(pheno, file="pheno", row.names=FALSE, sep=" ")