Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 94:89492de287a6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Fri, 01 Dec 2017 09:49:09 -0500
parents 06acadd38824
children f0c65c9f1078
comparison
equal deleted inserted replaced
93:06acadd38824 94:89492de287a6
572 start_date <- temperature_data_frame$DATE[1] 572 start_date <- temperature_data_frame$DATE[1]
573 end_date <- temperature_data_frame$DATE[opt$num_days] 573 end_date <- temperature_data_frame$DATE[opt$num_days]
574 574
575 # Subfigure 1: population size by life stage 575 # Subfigure 1: population size by life stage
576 title <- paste(opt$insect, ": Total pop. by life stage :", opt$location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ") 576 title <- paste(opt$insect, ": Total pop. by life stage :", opt$location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ")
577 plot(day.all, mean_value_adult, main=title, type="l", ylim=c(0, max(mean_value_egg + mean_value_egg.se, mean_value_nymph + mean_value_nymph.se, mean_value_adult + mean_value_adult.se)), axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3) 577 plot(day.all, mean_value_adult, main=title, type="l", ylim=c(0, max(mean_value_egg + mean_value_egg.std_error, mean_value_nymph + mean_value_nymph.std_error, mean_value_adult + mean_value_adult.std_error)), axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3)
578 # Young and old nymphs. 578 # Young and old nymphs.
579 lines(day.all, mean_value_nymph, lwd=2, lty=1, col=2) 579 lines(day.all, mean_value_nymph, lwd=2, lty=1, col=2)
580 # Eggs 580 # Eggs
581 lines(day.all, mean_value_egg, lwd=2, lty=1, col=4) 581 lines(day.all, mean_value_egg, lwd=2, lty=1, col=4)
582 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")) 582 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"))
584 leg.text <- c("Egg", "Nymph", "Adult") 584 leg.text <- c("Egg", "Nymph", "Adult")
585 legend("topleft", leg.text, lty=c(1, 1, 1), col=c(4, 2, 1), cex=3) 585 legend("topleft", leg.text, lty=c(1, 1, 1), col=c(4, 2, 1), cex=3)
586 if (opt$se_plot == 1) { 586 if (opt$se_plot == 1) {
587 # Add Standard error lines to plot 587 # Add Standard error lines to plot
588 # Standard error for adults 588 # Standard error for adults
589 lines (day.all, mean_value_adult+mean_value_adult.se, lty=2) 589 lines (day.all, mean_value_adult+mean_value_adult.std_error, lty=2)
590 lines (day.all, mean_value_adult-mean_value_adult.se, lty=2) 590 lines (day.all, mean_value_adult-mean_value_adult.std_error, lty=2)
591 # Standard error for nymphs 591 # Standard error for nymphs
592 lines (day.all, mean_value_nymph+mean_value_nymph.se, col=2, lty=2) 592 lines (day.all, mean_value_nymph+mean_value_nymph.std_error, col=2, lty=2)
593 lines (day.all, mean_value_nymph-mean_value_nymph.se, col=2, lty=2) 593 lines (day.all, mean_value_nymph-mean_value_nymph.std_error, col=2, lty=2)
594 # Standard error for eggs 594 # Standard error for eggs
595 lines (day.all, mean_value_egg+mean_value_egg.se, col=4, lty=2) 595 lines (day.all, mean_value_egg+mean_value_egg.std_error, col=4, lty=2)
596 lines (day.all, mean_value_egg-mean_value_egg.se, col=4, lty=2) 596 lines (day.all, mean_value_egg-mean_value_egg.std_error, col=4, lty=2)
597 } 597 }
598 598
599 # Subfigure 2: population size by generation 599 # Subfigure 2: population size by generation
600 title <- paste(opt$insect, ": Total pop. by generation :", opt$location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ") 600 title <- paste(opt$insect, ": Total pop. by generation :", opt$location, ": Lat:", latitude, ":", start_date, "-", end_date, sep=" ")
601 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) 601 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)