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comparison bmsb.R @ 11:99a386ac1f5b draft

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author greg
date Tue, 16 Aug 2016 09:52:16 -0400
parents ff341ead2c11
children 860730afa679
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10:303a662c7881 11:99a386ac1f5b
1 #!/usr/bin/env Rscript 1 #!/usr/bin/env Rscript
2 2
3 3 #suppressPackageStartupMessages(library("optparse"))
4 suppressPackageStartupMessages(require("hash")) 4 #suppressPackageStartupMessages(library("rjson"))
5 suppressPackageStartupMessages(require("KernSmooth"))
6 suppressPackageStartupMessages(require("methods"))
7 suppressPackageStartupMessages(library("optparse"))
8 suppressPackageStartupMessages(library("rjson"))
9 suppressPackageStartupMessages(require("utils"))
10
11 5
12 option_list <- list( 6 option_list <- list(
13 make_option(c("-s", "--save_log"), action="store_true", default=FALSE, help="Save R logs"), 7 make_option(c("-s", "--save_log"), action="store_true", default=FALSE, help="Save R logs"),
14 make_option(c("-m", "--output_r_log"), action="store", help="Output dataset for R logs"), 8 make_option(c("-m", "--output_r_log"), action="store", help="Output dataset for R logs"),
15 make_option(c("-o", "--output"), action="store", help="Output dataset") 9 make_option(c("-o", "--output"), action="store", help="Output dataset")
148 return 142 return
149 } 143 }
150 144
151 145
152 # model initialization 146 # model initialization
153 # TODO: setwd(“/home/lunarmouse/Nielsen's project/”) 147 # TODO: add tool params for the following options.
154 # start with 1000 individuals 148 # start with 1000 individuals
155 n <- 1000 149 n <- 1000
156 # Generation, Stage, DD, T, Diapause 150 # Generation, Stage, DD, T, Diapause
157 vec.ini <- c(0,3,0,0,0) 151 vec.ini <- c(0,3,0,0,0)
158 # overwintering, previttelogenic, DD = 0, T = 0, no-diapause 152 # overwintering, previttelogenic, DD = 0, T = 0, no-diapause
434 g2.adult[day] <- sum((vec.mat[,1] == 2 & vec.mat[,2] == 3) | (vec.mat[,1] == 2 & vec.mat[,2] == 4) | (vec.mat[,1] == 2 & vec.mat[,2] == 5)) 428 g2.adult[day] <- sum((vec.mat[,1] == 2 & vec.mat[,2] == 3) | (vec.mat[,1] == 2 & vec.mat[,2] == 4) | (vec.mat[,1] == 2 & vec.mat[,2] == 5))
435 N.newborn[day] <- n.newborn 429 N.newborn[day] <- n.newborn
436 N.death[day] <- n.death 430 N.death[day] <- n.death
437 N.adult[day] <- n.adult 431 N.adult[day] <- n.adult
438 } 432 }
439 print(n.sim) 433 #print(n.sim)
440 } 434 }
441 435
442 proc.time() - ptm 436 proc.time() - ptm
443 dd.cum <- cumsum(dd.day) 437 dd.cum <- cumsum(dd.day)
444 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") 438 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)