# HG changeset patch
# User greg
# Date 1481901360 18000
# Node ID 7c40c2b303f1ecc615165a37256a31af7e06baf3
# Parent  7c43bc0ce69c4943ad38935dfaa1c0ff81890b07
Uploaded

diff -r 7c43bc0ce69c -r 7c40c2b303f1 bmsb.R
--- a/bmsb.R	Fri Dec 16 08:51:06 2016 -0500
+++ b/bmsb.R	Fri Dec 16 10:16:00 2016 -0500
@@ -4,12 +4,12 @@
 
 option_list <- list(
     make_option(c("-a", "--adult_mort"), action="store", dest="adult_mort", type="integer", help="Adjustment rate for adult mortality"),
-    make_option(c("-b", "--adult_nymph_accum"), action="store", dest="adult_nymph_accum", type="integer", help="Adjustment of DD accumulation (old nymph->adult)"),
+    make_option(c("-b", "--adult_accum"), action="store", dest="adult_accum", type="integer", help="Adjustment of DD accumulation (old nymph->adult)"),
     make_option(c("-c", "--egg_mort"), action="store", dest="egg_mort", type="integer", help="Adjustment rate for egg mortality"),
     make_option(c("-d", "--latitude"), action="store", dest="latitude", type="double", help="Latitude of selected location"),
     make_option(c("-e", "--location"), action="store", dest="location", help="Selected location"),
     make_option(c("-f", "--min_clutch_size"), action="store", dest="min_clutch_size", type="integer", help="Adjustment of minimum clutch size"),
-    make_option(c("-g", "--max_clutch_size"), action="store", dest="max_clutch_size", type="integer", help="Adjustment of maximum clutch size"),
+    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("-o", "--output"), action="store", dest="output", help="Output dataset"),
@@ -207,6 +207,18 @@
     return
 }
 
+cat("Replications: ", opt$replications, "\n")
+cat("Photoperiod: ", opt$photoperiod, "\n")
+cat("Oviposition rate: ", opt$oviposition, "\n")
+cat("Egg mortality rate: ", opt$egg_mort, "\n")
+cat("Nymph mortality rate: ", opt$nymph_mort, "\n")
+cat("Adult mortality rate: ", opt$adult_mort, "\n")
+cat("Min clutch size: ", opt$min_clutch_size, "\n")
+cat("Max clutch size: ", opt$max_clutch_size, "\n")
+cat("(egg->young nymph): ", opt$young_nymph_accum, "\n")
+cat("(young nymph->old nymph): ", opt$old_nymph_accum, "\n")
+cat("(old nymph->adult): ", opt$adult_accum, "\n")
+
 # Read in the input temperature datafile
 temperature_file_path <- data.input(opt$location, opt$year, opt$temperature_dataset)
 
@@ -619,7 +631,7 @@
 # SE for nymphs
 sn.se <- apply((S1.rep + S2.rep) / sqrt(opt$replications), 1, sd)
 # SE for eggs
-se.se <- apply(S0.rep ,1 ,sd) / sqrt(opt$replications)
+se.se <- apply(S0.rep, 1, sd) / sqrt(opt$replications)
 # SE value for P
 g0.se <- apply(g0.rep, 1, sd) / sqrt(opt$replications)
 # SE for F1
@@ -633,7 +645,7 @@
 # SE for F2 adult
 g2a.se <- apply(g2a.rep, 1, sd) / sqrt(opt$replications)
 
-dev.new(width = 9, height = 9)
+dev.new(width=20, height=20)
 
 # Start PDF device driver to save charts to output.
 pdf(file=opt$output, height=20, width=20, bg="white")