Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 48:66712cdec7c0 draft

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author greg
date Mon, 13 Nov 2017 11:05:42 -0500
parents d6482112bf35
children d03ba99e25b6
comparison
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47:d6482112bf35 48:66712cdec7c0
577 # SE for F1 adult 577 # SE for F1 adult
578 g1a.se <- apply(g1a.rep, 1, sd) / sqrt(opt$replications) 578 g1a.se <- apply(g1a.rep, 1, sd) / sqrt(opt$replications)
579 # SE for F2 adult 579 # SE for F2 adult
580 g2a.se <- apply(g2a.rep, 1, sd) / sqrt(opt$replications) 580 g2a.se <- apply(g2a.rep, 1, sd) / sqrt(opt$replications)
581 581
582 dev.new(width=20, height=20) 582 dev.new(width=20, height=30)
583 583
584 # Start PDF device driver to save charts to output. 584 # Start PDF device driver to save charts to output.
585 pdf(file=opt$output, height=20, width=20, bg="white") 585 pdf(file=opt$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 2: population size by life stage
590 title <- paste("BSMB Total Population Size by Life Stage:", opt$location, ", Latitude:", latitude, ", Temperature Dates:", start_date, "to", end_date, sep=" ") 590 title <- paste("BSMB Total Population Size by Life Stage:", opt$location, ", Latitude:", latitude, ", Temperature Dates:", 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=2, cex.lab=2, cex.axis=2, cex.main=2) 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=2, cex.axis=2, cex.main=2)
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=2, 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=2, labels=c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"))
597 axis(2, cex.axis = 2) 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=2) 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
603 lines (day.all, sa + sa.se, lty=2) 603 lines (day.all, sa + sa.se, lty=2)
604 lines (day.all, sa - sa.se, lty=2) 604 lines (day.all, sa - sa.se, lty=2)
605 # SE for nymphs 605 # SE for nymphs
606 lines (day.all, sn + sn.se, col=2, lty=2) 606 lines (day.all, sn + sn.se, col=2, lty=2)
607 lines (day.all, sn - sn.se, col=2, lty=2) 607 lines (day.all, sn - sn.se, col=2, lty=2)
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 3: population size by generation
614 title <- paste("BSMB Total Population Size by Generation:", opt$location, ", Latitude:", latitude, ", Temperature Dates:", start_date, "to", end_date, sep=" ") 614 title <- paste("BSMB Total Population Size by Generation:", opt$location, ", Latitude:", latitude, ", Temperature Dates:", 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=2, cex.lab=2, cex.axis=2, cex.main=2) 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=2, cex.axis=2, cex.main=2)
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 = 2, 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 = 2, labels = c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"))
619 axis(2, cex.axis = 2) 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 = 2) 621 legend("topleft", leg.text, lty = c(1, 1, 1), col =c(1, 2, 4), cex = 2)
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)
627 # SE for nymphs 627 # SE for nymphs
628 lines (day.all, g1 + g1.se, col = 2, lty = 2) 628 lines (day.all, g1 + g1.se, col = 2, lty = 2)
629 lines (day.all, g1 - g1.se, col = 2, lty = 2) 629 lines (day.all, g1 - g1.se, col = 2, 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 4: adult population size by generation
636 title <- paste("BSMB Adult Population Size by Generation:", opt$location, ", Latitude:", latitude, ", Temperature Dates:", start_date, "to", end_date, sep=" ") 636 title <- paste("BSMB Adult Population Size by Generation:", opt$location, ", Latitude:", latitude, ", Temperature Dates:", 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=2, cex.lab=2, cex.axis=2, cex.main=2) 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=2, cex.axis=2, cex.main=2)
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 = 2, 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 = 2, labels = c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"))
641 axis(2, cex.axis = 2) 641 axis(2, cex.axis = 2)
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 = 2) 643 legend("topleft", leg.text, lty = c(1, 1, 1), col = c(1, 2, 4), cex = 2)
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)
649 # SE for nymphs 649 # SE for nymphs
650 lines (day.all, g1a + g1a.se, col = 2, lty = 2) 650 lines (day.all, g1a + g1a.se, col = 2, lty = 2)
651 lines (day.all, g1a - g1a.se, col = 2, lty = 2) 651 lines (day.all, g1a - g1a.se, col = 2, lty = 2)
652 # SE for eggs 652 # SE for eggs
653 lines (day.all, g2a + g2a.se, col = 4, lty = 2) 653 lines (day.all, g2a + g2a.se, col = 4, lty = 2)
654 lines (day.all, g2a - g2a.se, col = 4, lty = 2) 654 lines (day.all, g2a - g2a.se, col = 4, lty = 2)
655 } 655 }
656 656
657 # Turn off device driver to flush output. 657 # Turn off device driver to flush output.
658 dev.off() 658 dev.off()