Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 39:e7bb2a00d30d draft

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author greg
date Thu, 09 Nov 2017 14:00:02 -0500
parents b81d2443b1b8
children ece79df73287
comparison
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38:b81d2443b1b8 39:e7bb2a00d30d
205 raw_data_matrix <- matrix(rep(0, opt$num_days * 6), nrow=opt$num_days) 205 raw_data_matrix <- matrix(rep(0, opt$num_days * 6), nrow=opt$num_days)
206 temperature_file_path <- convert_csv_to_rdata(temperature_data, raw_data_matrix) 206 temperature_file_path <- convert_csv_to_rdata(temperature_data, raw_data_matrix)
207 latitude <- temperature_data[1, 1] 207 latitude <- temperature_data[1, 1]
208 208
209 cat("Number of days: ", opt$num_days, "\n") 209 cat("Number of days: ", opt$num_days, "\n")
210 cat("Latitude: ", latitude, "\n")
211 cat("Replications: ", opt$replications, "\n")
212 210
213 # Initialize matrix for results from all replications. 211 # Initialize matrix for results from all replications.
214 S0.rep <- S1.rep <- S2.rep <- S3.rep <- S4.rep <- S5.rep <- matrix(rep(0, opt$num_days * opt$replications), ncol = opt$replications) 212 S0.rep <- S1.rep <- S2.rep <- S3.rep <- S4.rep <- S5.rep <- matrix(rep(0, opt$num_days * opt$replications), ncol = opt$replications)
215 newborn.rep <- death.rep <- adult.rep <- pop.rep <- g0.rep <- g1.rep <- g2.rep <- g0a.rep <- g1a.rep <- g2a.rep <- matrix(rep(0, opt$num_days * opt$replications), ncol=opt$replications) 213 newborn.rep <- death.rep <- adult.rep <- pop.rep <- g0.rep <- g1.rep <- g2.rep <- g0a.rep <- g1a.rep <- g2a.rep <- matrix(rep(0, opt$num_days * opt$replications), ncol=opt$replications)
216 214
586 pdf(file=opt$output, height=20, width=20, bg="white") 584 pdf(file=opt$output, height=20, width=20, bg="white")
587 585
588 par(mar = c(5, 6, 4, 4), mfrow=c(3, 1)) 586 par(mar = c(5, 6, 4, 4), mfrow=c(3, 1))
589 587
590 # Subfigure 2: population size by life stage 588 # Subfigure 2: population size by life stage
591 title <- paste(opt$location, start_date, "to", end_date, "BSMB Total Population Size by Life Stage", sep=" ") 589 title <- paste("BSMB Total Population Size by Life Stage:", opt$location, ", Latitude:", latitude, ", Temperature Dates:", start_date, "to", end_date, sep=" ")
592 plot(day.all, sa, main=title, type="l", ylim=c(0, max(se + se.se, sn + sn.se, sa + sa.se)), axes=F, lwd=2, xlab="", ylab="Number", cex=2, cex.lab=2, cex.axis=2, cex.main=2) 590 plot(day.all, sa, main=title, type="l", ylim=c(0, max(se + se.se, sn + sn.se, sa + sa.se)), axes=F, lwd=2, xlab="", ylab="Number", cex=2, cex.lab=2, cex.axis=2, cex.main=2)
593 # Young and old nymphs. 591 # Young and old nymphs.
594 lines(day.all, sn, lwd=2, lty=1, col=2) 592 lines(day.all, sn, lwd=2, lty=1, col=2)
595 # Eggs 593 # Eggs
596 lines(day.all, se, lwd=2, lty=1, col=4) 594 lines(day.all, se, lwd=2, lty=1, col=4)
610 lines (day.all, se + se.se, col=4, lty=2) 608 lines (day.all, se + se.se, col=4, lty=2)
611 lines (day.all, se - se.se, col=4, lty=2) 609 lines (day.all, se - se.se, col=4, lty=2)
612 } 610 }
613 611
614 # Subfigure 3: population size by generation 612 # Subfigure 3: population size by generation
615 title <- paste(opt$location, start_date, "to", end_date, "BSMB Total Population Size by Generation", sep=" ") 613 title <- paste("BSMB Total Population Size by Generation:", opt$location, Latitude:", latitude, Temperature Dates:", start_date, "to", end_date, sep=" ")
616 plot(day.all, g0, main=title, type="l", ylim=c(0, max(g2)), axes=F, lwd=2, xlab="", ylab="Number", cex=2, cex.lab=2, cex.axis=2, cex.main=2) 614 plot(day.all, g0, main=title, type="l", ylim=c(0, max(g2)), axes=F, lwd=2, xlab="", ylab="Number", cex=2, cex.lab=2, cex.axis=2, cex.main=2)
617 lines(day.all, g1, lwd = 2, lty = 1, col = 2) 615 lines(day.all, g1, lwd = 2, lty = 1, col = 2)
618 lines(day.all, g2, lwd = 2, lty = 1, col = 4) 616 lines(day.all, g2, lwd = 2, lty = 1, col = 4)
619 axis(1, at = c(1:12) * 30 - 15, cex.axis = 2, labels = c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec")) 617 axis(1, at = c(1:12) * 30 - 15, cex.axis = 2, labels = c("Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec"))
620 axis(2, cex.axis = 2) 618 axis(2, cex.axis = 2)
632 lines (day.all, g2 + g2.se, col = 4, lty = 2) 630 lines (day.all, g2 + g2.se, col = 4, lty = 2)
633 lines (day.all, g2 - g2.se, col = 4, lty = 2) 631 lines (day.all, g2 - g2.se, col = 4, lty = 2)
634 } 632 }
635 633
636 # Subfigure 4: adult population size by generation 634 # Subfigure 4: adult population size by generation
637 title <- paste(opt$location, start_date, "to", end_date, "BSMB Adult Population Size by Generation", sep=" ") 635 title <- paste("BSMB Adult Population Size by Generation:", opt$location, Latitude:", latitude, Temperature Dates:", start_date, "to", end_date, sep=" ")
638 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) 636 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)
639 lines(day.all, g1a, lwd = 2, lty = 1, col = 2) 637 lines(day.all, g1a, lwd = 2, lty = 1, col = 2)
640 lines(day.all, g2a, lwd = 2, lty = 1, col = 4) 638 lines(day.all, g2a, lwd = 2, lty = 1, col = 4)
641 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")) 639 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"))
642 axis(2, cex.axis = 2) 640 axis(2, cex.axis = 2)