--- a/insect_phenology_model.R	Tue Nov 14 14:49:23 2017 -0500
+++ b/insect_phenology_model.R	Tue Nov 14 14:49:29 2017 -0500
@@ -11,7 +11,6 @@
     make_option(c("-i", "--max_clutch_size"), action="store", dest="max_clutch_size", type="integer", help="Adjustment of maximum clutch size"),
     make_option(c("-j", "--nymph_mort"), action="store", dest="nymph_mort", type="integer", help="Adjustment rate for nymph mortality"),
     make_option(c("-k", "--old_nymph_accum"), action="store", dest="old_nymph_accum", type="integer", help="Adjustment of DD accumulation (young nymph->old nymph)"),
-    make_option(c("-m", "--num_columns"), action="store", dest="num_columns", type="integer", help="Total number of columns in the temperature dataset"),
     make_option(c("-n", "--num_days"), action="store", dest="num_days", type="integer", help="Total number of days in the temperature dataset"),
     make_option(c("-o", "--output"), action="store", dest="output", help="Output dataset"),
     make_option(c("-p", "--oviposition"), action="store", dest="oviposition", type="integer", help="Adjustment for oviposition rate"),
@@ -26,10 +25,10 @@
 args <- parse_args(parser, positional_arguments=TRUE)
 opt <- args$options
 
-parse_input_data = function(input_file, num_rows, num_columns) {
+parse_input_data = function(input_file, num_rows) {
     # Read in the input temperature datafile into a data frame.
     temperature_data_frame <- read.csv(file=input_file, header=T, strip.white=TRUE, sep=",")
-    if (num_columns == 6) {
+    if (ncol(temperature_data_frame) == 6) {
         # The input data has the following 6 columns:
         # LATITUDE, LONGITUDE, DATE, DOY, TMIN, TMAX
         # Add a column containing the daylight length for each day.
@@ -201,9 +200,7 @@
     return
 }
 
-cat("Number of columns: ", opt$num_columns, "\n")
-
-temperature_data_frame <- parse_input_data(opt$input, opt$num_days, opt$num_columns)
+temperature_data_frame <- parse_input_data(opt$input, opt$num_days)
 print(temperature_data_frame)
 latitude <- temperature_data_frame[1, 1]