Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 87:522fe34a1dfc draft

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author greg
date Wed, 22 Nov 2017 13:14:08 -0500
parents 8f5c05be4efe
children b387ea636ff8
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86:5e1f9fde280c 87:522fe34a1dfc
16 make_option(c("-p", "--oviposition"), action="store", dest="oviposition", type="integer", help="Adjustment for oviposition rate"), 16 make_option(c("-p", "--oviposition"), action="store", dest="oviposition", type="integer", help="Adjustment for oviposition rate"),
17 make_option(c("-q", "--photoperiod"), action="store", dest="photoperiod", type="double", help="Critical photoperiod for diapause induction/termination"), 17 make_option(c("-q", "--photoperiod"), action="store", dest="photoperiod", type="double", help="Critical photoperiod for diapause induction/termination"),
18 make_option(c("-s", "--replications"), action="store", dest="replications", type="integer", help="Number of replications"), 18 make_option(c("-s", "--replications"), action="store", dest="replications", type="integer", help="Number of replications"),
19 make_option(c("-t", "--se_plot"), action="store", dest="se_plot", help="Plot SE"), 19 make_option(c("-t", "--se_plot"), action="store", dest="se_plot", help="Plot SE"),
20 make_option(c("-v", "--input"), action="store", dest="input", help="Temperature data for selected location"), 20 make_option(c("-v", "--input"), action="store", dest="input", help="Temperature data for selected location"),
21 make_option(c("-y", "--young_nymph_accum"), action="store", dest="young_nymph_accum", type="integer", help="Adjustment of DD accumulation (egg->young nymph)") 21 make_option(c("-y", "--young_nymph_accum"), action="store", dest="young_nymph_accum", type="integer", help="Adjustment of DD accumulation (egg->young nymph)"),
22 make_option(c("-x", "--insect"), action="store", dest="insect", help="Insect name")
22 ) 23 )
23 24
24 parser <- OptionParser(usage="%prog [options] file", option_list=option_list) 25 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
25 args <- parse_args(parser, positional_arguments=TRUE) 26 args <- parse_args(parser, positional_arguments=TRUE)
26 opt <- args$options 27 opt <- args$options
573 pdf(file=opt$output, width=20, height=30, bg="white") 574 pdf(file=opt$output, width=20, height=30, bg="white")
574 575
575 par(mar = c(5, 6, 4, 4), mfrow=c(3, 1)) 576 par(mar = c(5, 6, 4, 4), mfrow=c(3, 1))
576 577
577 # Subfigure 1: population size by life stage 578 # Subfigure 1: population size by life stage
578 title <- paste("BSMB total population by life stage :", opt$location, ": Lat:", latitude, ":", start_date, "to", end_date, sep=" ") 579 title <- paste("opt$insect : Total pop. by life stage :", opt$location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ")
579 plot(day.all, sa, main=title, type="l", ylim=c(0, max(se + se.se, sn + sn.se, sa + sa.se)), axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3) 580 plot(day.all, sa, main=title, type="l", ylim=c(0, max(se + se.se, sn + sn.se, sa + sa.se)), axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3)
580 # Young and old nymphs. 581 # Young and old nymphs.
581 lines(day.all, sn, lwd=2, lty=1, col=2) 582 lines(day.all, sn, lwd=2, lty=1, col=2)
582 # Eggs 583 # Eggs
583 lines(day.all, se, lwd=2, lty=1, col=4) 584 lines(day.all, se, lwd=2, lty=1, col=4)
597 lines (day.all, se + se.se, col=4, lty=2) 598 lines (day.all, se + se.se, col=4, lty=2)
598 lines (day.all, se - se.se, col=4, lty=2) 599 lines (day.all, se - se.se, col=4, lty=2)
599 } 600 }
600 601
601 # Subfigure 2: population size by generation 602 # Subfigure 2: population size by generation
602 title <- paste("BSMB total population by generation :", opt$location, ": Lat:", latitude, ":", start_date, "to", end_date, sep=" ") 603 title <- paste("opt$insect : Total pop. by generation :", opt$location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ")
603 plot(day.all, g0, main=title, type="l", ylim=c(0, max(g2)), axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3) 604 plot(day.all, g0, main=title, type="l", ylim=c(0, max(g2)), axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3)
604 lines(day.all, g1, lwd = 2, lty = 1, col=2) 605 lines(day.all, g1, lwd = 2, lty = 1, col=2)
605 lines(day.all, g2, lwd = 2, lty = 1, col=4) 606 lines(day.all, g2, lwd = 2, lty = 1, col=4)
606 axis(1, at=c(1:12) * 30 - 15, cex.axis=3, labels = c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec")) 607 axis(1, at=c(1:12) * 30 - 15, cex.axis=3, labels = c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"))
607 axis(2, cex.axis=3) 608 axis(2, cex.axis=3)
619 lines (day.all, g2+g2.se, col=4, lty=2) 620 lines (day.all, g2+g2.se, col=4, lty=2)
620 lines (day.all, g2-g2.se, col=4, lty=2) 621 lines (day.all, g2-g2.se, col=4, lty=2)
621 } 622 }
622 623
623 # Subfigure 3: adult population size by generation 624 # Subfigure 3: adult population size by generation
624 title <- paste("BSMB adult population by generation :", opt$location, ": Lat:", latitude, ":", start_date, "to", end_date, sep=" ") 625 title <- paste("opt$insect : Adult pop. by generation :", opt$location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ")
625 plot(day.all, g0a, ylim=c(0, max(g2a) + 100), main=title, type="l", axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3) 626 plot(day.all, g0a, ylim=c(0, max(g2a) + 100), main=title, type="l", axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3)
626 lines(day.all, g1a, lwd = 2, lty = 1, col=2) 627 lines(day.all, g1a, lwd = 2, lty = 1, col=2)
627 lines(day.all, g2a, lwd = 2, lty = 1, col=4) 628 lines(day.all, g2a, lwd = 2, lty = 1, col=4)
628 axis(1, at=c(1:12) * 30 - 15, cex.axis=3, labels = c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec")) 629 axis(1, at=c(1:12) * 30 - 15, cex.axis=3, labels = c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"))
629 axis(2, cex.axis=3) 630 axis(2, cex.axis=3)