Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 54:5115076f136c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Mon, 13 Nov 2017 11:44:38 -0500
parents 9dc9dc41851b
children c24b519ad05e
comparison
equal deleted inserted replaced
53:9dc9dc41851b 54:5115076f136c
584 # Start PDF device driver to save charts to output. 584 # Start PDF device driver to save charts to output.
585 pdf(file=opt$output, width=20, height=30, bg="white") 585 pdf(file=opt$output, width=20, height=30, bg="white")
586 586
587 par(mar = c(5, 6, 4, 4), mfrow=c(3, 1)) 587 par(mar = c(5, 6, 4, 4), mfrow=c(3, 1))
588 588
589 # Subfigure 2: population size by life stage 589 # Subfigure 1: population size by life stage
590 title <- paste("BSMB Total Population Size by Life Stage |", opt$location, "| Lat:", latitude, "|", start_date, "to", end_date, sep=" ") 590 title <- paste("BSMB total population by life stage :", opt$location, ": Lat:", latitude, ":", start_date, "to", end_date, sep=" ")
591 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="Number", cex=3, cex.lab=3, cex.axis=3, cex.main=3) 591 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="total population", cex=3, cex.lab=3, cex.axis=3, cex.main=3)
592 # Young and old nymphs. 592 # Young and old nymphs.
593 lines(day.all, sn, lwd=2, lty=1, col=2) 593 lines(day.all, sn, lwd=2, lty=1, col=2)
594 # Eggs 594 # Eggs
595 lines(day.all, se, lwd=2, lty=1, col=4) 595 lines(day.all, se, lwd=2, lty=1, col=4)
596 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")) 596 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"))
597 axis(2, cex.axis = 3) 597 axis(2, cex.axis=3)
598 leg.text <- c("Egg", "Nymph", "Adult") 598 leg.text <- c("Egg", "Nymph", "Adult")
599 legend("topleft", leg.text, lty=c(1, 1, 1), col=c(4, 2, 1), cex=3) 599 legend("topleft", leg.text, lty=c(1, 1, 1), col=c(4, 2, 1), cex=3)
600 if (opt$se_plot == 1) { 600 if (opt$se_plot == 1) {
601 # Add SE lines to plot 601 # Add SE lines to plot
602 # SE for adults 602 # SE for adults
608 # SE for eggs 608 # SE for eggs
609 lines (day.all, se + se.se, col=4, lty=2) 609 lines (day.all, se + se.se, col=4, lty=2)
610 lines (day.all, se - se.se, col=4, lty=2) 610 lines (day.all, se - se.se, col=4, lty=2)
611 } 611 }
612 612
613 # Subfigure 3: population size by generation 613 # Subfigure 2: population size by generation
614 title <- paste("BSMB Total Population Size by Generation |", opt$location, "| Lat:", latitude, "|", start_date, "to", end_date, sep=" ") 614 title <- paste("BSMB total population by generation :", opt$location, ": Lat:", latitude, ":", start_date, "to", end_date, sep=" ")
615 plot(day.all, g0, main=title, type="l", ylim=c(0, max(g2)), axes=F, lwd=2, xlab="", ylab="Number", cex=3, cex.lab=3, cex.axis=3, cex.main=3) 615 plot(day.all, g0, main=title, type="l", ylim=c(0, max(g2)), axes=F, lwd=2, xlab="", ylab="total population", cex=3, cex.lab=3, cex.axis=3, cex.main=3)
616 lines(day.all, g1, lwd = 2, lty = 1, col = 2) 616 lines(day.all, g1, lwd = 2, lty = 1, col = 2)
617 lines(day.all, g2, lwd = 2, lty = 1, col = 4) 617 lines(day.all, g2, lwd = 2, lty = 1, col = 4)
618 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")) 618 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"))
619 axis(2, cex.axis = 3) 619 axis(2, cex.axis=3)
620 leg.text <- c("P", "F1", "F2") 620 leg.text <- c("P", "F1", "F2")
621 legend("topleft", leg.text, lty = c(1, 1, 1), col =c(1, 2, 4), cex=3) 621 legend("topleft", leg.text, lty=c(1, 1, 1), col=c(1, 2, 4), cex=3)
622 if (opt$se_plot == 1) { 622 if (opt$se_plot == 1) {
623 # Add SE lines to plot 623 # Add SE lines to plot
624 # SE for adults 624 # SE for adults
625 lines (day.all, g0 + g0.se, lty = 2) 625 lines (day.all, g0 + g0.se, lty = 2)
626 lines (day.all, g0 - g0.se, lty = 2) 626 lines (day.all, g0 - g0.se, lty = 2)
630 # SE for eggs 630 # SE for eggs
631 lines (day.all, g2 + g2.se, col = 4, lty = 2) 631 lines (day.all, g2 + g2.se, col = 4, lty = 2)
632 lines (day.all, g2 - g2.se, col = 4, lty = 2) 632 lines (day.all, g2 - g2.se, col = 4, lty = 2)
633 } 633 }
634 634
635 # Subfigure 4: adult population size by generation 635 # Subfigure 3: adult population size by generation
636 title <- paste("BSMB Adult Population Size by Generation |", opt$location, "| Lat:", latitude, "|", start_date, "to", end_date, sep=" ") 636 title <- paste("BSMB adult population by generation :", opt$location, ": Lat:", latitude, ":", start_date, "to", end_date, sep=" ")
637 plot(day.all, g0a, ylim=c(0, max(g2a) + 100), main=title, type="l", axes=F, lwd=2, xlab="Year", ylab="Number", cex=3, cex.lab=3, cex.axis=3, cex.main=3) 637 plot(day.all, g0a, ylim=c(0, max(g2a) + 100), main=title, type="l", axes=F, lwd=2, xlab="", ylab="adult population", cex=3, cex.lab=3, cex.axis=3, cex.main=3)
638 lines(day.all, g1a, lwd = 2, lty = 1, col = 2) 638 lines(day.all, g1a, lwd = 2, lty = 1, col = 2)
639 lines(day.all, g2a, lwd = 2, lty = 1, col = 4) 639 lines(day.all, g2a, lwd = 2, lty = 1, col = 4)
640 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")) 640 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"))
641 axis(2, cex.axis = 3) 641 axis(2, cex.axis=3)
642 leg.text <- c("P", "F1", "F2") 642 leg.text <- c("P", "F1", "F2")
643 legend("topleft", leg.text, lty = c(1, 1, 1), col = c(1, 2, 4), cex=3) 643 legend("topleft", leg.text, lty=c(1, 1, 1), col=c(1, 2, 4), cex=3)
644 if (opt$se_plot == 1) { 644 if (opt$se_plot == 1) {
645 # Add SE lines to plot 645 # Add SE lines to plot
646 # SE for adults 646 # SE for adults
647 lines (day.all, g0a + g0a.se, lty = 2) 647 lines (day.all, g0a + g0a.se, lty = 2)
648 lines (day.all, g0a - g0a.se, lty = 2) 648 lines (day.all, g0a - g0a.se, lty = 2)