# HG changeset patch
# User greg
# Date 1471355536 14400
# Node ID 99a386ac1f5b38fff5720571de8e83e3f9ab9fc9
# Parent  303a662c788170a7eb8286ff948bfb09d0ddba05
Uploaded

diff -r 303a662c7881 -r 99a386ac1f5b bmsb.R
--- a/bmsb.R	Fri Aug 12 14:45:12 2016 -0400
+++ b/bmsb.R	Tue Aug 16 09:52:16 2016 -0400
@@ -1,13 +1,7 @@
 #!/usr/bin/env Rscript
 
-
-suppressPackageStartupMessages(require("hash"))
-suppressPackageStartupMessages(require("KernSmooth"))
-suppressPackageStartupMessages(require("methods"))
-suppressPackageStartupMessages(library("optparse"))
-suppressPackageStartupMessages(library("rjson"))
-suppressPackageStartupMessages(require("utils"))
-
+#suppressPackageStartupMessages(library("optparse"))
+#suppressPackageStartupMessages(library("rjson"))
 
 option_list <- list(
     make_option(c("-s", "--save_log"), action="store_true", default=FALSE, help="Save R logs"),
@@ -150,7 +144,7 @@
 
 
 # model initialization
-# TODO: setwd(“/home/lunarmouse/Nielsen's project/”)
+# TODO: add tool params for the following options.
 # start with 1000 individuals
 n <- 1000
 # Generation, Stage, DD, T, Diapause
@@ -436,9 +430,9 @@
         N.death[day] <- n.death
         N.adult[day] <- n.adult
     }   
-print(n.sim)
+#print(n.sim)
 }
 
 proc.time() - ptm
 dd.cum <- cumsum(dd.day)
-save(dd.day, dd.cum, S0, S1, S2, S3, S4, S5, N.newborn, N.death, N.adult, tot.pop, gen0.pop, gen1.pop, gen2.pop, g0.adult, g1.adult, g2.adult, file="asheville2014sim.Rdat")
+save(dd.day, dd.cum, S0, S1, S2, S3, S4, S5, N.newborn, N.death, N.adult, tot.pop, gen0.pop, gen1.pop, gen2.pop, g0.adult, g1.adult, g2.adult, file=opt$output)