Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 104:d6e37828b094 draft

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author greg
date Tue, 05 Dec 2017 11:13:23 -0500
parents 4d9e40d8af0f
children aa1890120743
comparison
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103:4d9e40d8af0f 104:d6e37828b094
627 pdf(file=opt$output, width=20, height=40, bg="white") 627 pdf(file=opt$output, width=20, height=40, bg="white")
628 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)) 628 par(mar=c(5, 6, 4, 4), mfrow=c(3, 1))
629 629
630 # Data analysis and visualization plots 630 # Data analysis and visualization plots
631 # only within a single calendar year. 631 # only within a single calendar year.
632 day.all <- c(1:opt$num_days) 632 days <- c(1:opt$num_days)
633 start_date <- temperature_data_frame$DATE[1] 633 start_date <- temperature_data_frame$DATE[1]
634 end_date <- temperature_data_frame$DATE[opt$num_days] 634 end_date <- temperature_data_frame$DATE[opt$num_days]
635 635
636 # Subfigure 1: population size by life stage 636 # Subfigure 1: population size by life stage
637 maxval <- max(eggs+eggs.std_error, nymphs+nymphs.std_error, adults+adults.std_error) 637 maxval <- max(eggs+eggs.std_error, nymphs+nymphs.std_error, adults+adults.std_error)
638 render_chart("pop_size_by_life_stage", opt$insect, opt$location, latitude, start_date, end_date, days.all, maxval, 638 render_chart("pop_size_by_life_stage", opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
639 opt$std_error_plot, adults, nymphs, eggs, adults.std_error, nymphs.std_error, eggs.std_error) 639 opt$std_error_plot, adults, nymphs, eggs, adults.std_error, nymphs.std_error, eggs.std_error)
640
641 # Subfigure 2: population size by generation 640 # Subfigure 2: population size by generation
642 maxval <- max(F2) 641 maxval <- max(F2)
643 render_chart("pop_size_by_generation", opt$insect, opt$location, latitude, start_date, end_date, days.all, maxval, 642 render_chart("pop_size_by_generation", opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
644 opt$std_error_plot, P, F1, F2, P.std_error, F1.std_error, F2.std_error) 643 opt$std_error_plot, P, F1, F2, P.std_error, F1.std_error, F2.std_error)
645
646
647 # Subfigure 3: adult population size by generation 644 # Subfigure 3: adult population size by generation
648 maxval <- max(F2_adults) + 100 645 maxval <- max(F2_adults) + 100
649 render_chart("adult_pop_size_by_generation", opt$insect, opt$location, latitude, start_date, end_date, days.all, maxval, 646 render_chart("adult_pop_size_by_generation", opt$insect, opt$location, latitude, start_date, end_date, days, maxval,
650 opt$std_error_plot, P_adults, F1_adults, F2_adults, P_adults.std_error, F1_adults.std_error, F2_adults2.std_error) 647 opt$std_error_plot, P_adults, F1_adults, F2_adults, P_adults.std_error, F1_adults.std_error, F2_adults2.std_error)
651
652 648
653 # Turn off device driver to flush output. 649 # Turn off device driver to flush output.
654 dev.off() 650 dev.off()