--- a/bmsb.R	Tue Aug 16 09:52:25 2016 -0400
+++ b/bmsb.R	Tue Aug 16 10:03:49 2016 -0400
@@ -3,12 +3,17 @@
 #suppressPackageStartupMessages(library("optparse"))
 #suppressPackageStartupMessages(library("rjson"))
 
-option_list <- list(
+options_list <- list(
     make_option(c("-s", "--save_log"), action="store_true", default=FALSE, help="Save R logs"),
     make_option(c("-m", "--output_r_log"), action="store", help="Output dataset for R logs"),
     make_option(c("-o", "--output"), action="store", help="Output dataset")
 )
 
+parser <- OptionParser(usage="%prog [options] file", options_list)
+args <- parse_args(parser, positional_arguments=TRUE)
+opt <- args$options
+
+
 daylength = function(L){
     # from Forsythe 1995
     p = 0.8333