Mercurial > repos > greg > insect_phenology_model
changeset 19:3c6e94e477cb draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 06 Mar 2018 14:26:45 -0500 |
| parents | f5ecff4800f2 |
| children | 214217142600 |
| files | insect_phenology_model.R |
| diffstat | 1 files changed, 26 insertions(+), 59 deletions(-) [+] |
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--- a/insect_phenology_model.R Tue Mar 06 13:39:14 2018 -0500 +++ b/insect_phenology_model.R Tue Mar 06 14:26:45 2018 -0500 @@ -52,38 +52,6 @@ return(temperature_data_frame); } -dev.egg = function(temperature) { - # This function is not used, but was - # in the original, so keep it for now. - dev.rate = -0.9843 * temperature + 33.438; - return(dev.rate); -} - -dev.emerg = function(temperature) { - # This function is not used, but was - # in the original, so keep it for now. - emerg.rate = -0.5332 * temperature + 24.147; - return(emerg.rate); -} - -dev.old = function(temperature) { - # This function is not used, but was - # in the original, so keep it for now. - n34 = -0.6119 * temperature + 17.602; - n45 = -0.4408 * temperature + 19.036; - dev.rate = mean(n34 + n45); - return(dev.rate); -} - -dev.young = function(temperature) { - # This function is not used, but was - # in the original, so keep it for now. - n12 = -0.3728 * temperature + 14.68; - n23 = -0.6119 * temperature + 25.249; - dev.rate = mean(n12 + n23); - return(dev.rate); -} - get_date_labels = function(temperature_data_frame, num_rows) { # Keep track of the years to see if spanning years. month_labels = list(); @@ -103,6 +71,22 @@ return(c(unlist(month_labels))); } + +get_file_path = function(life_stage, base_name, life_stage_nymph=NULL, life_stage_adult=NULL) { + if (!is.null(life_stage_nymph)) { + lsi = get_life_stage_index(life_stage, life_stage_nymph=life_stage_nymph); + file_name = paste(lsi, tolower(life_stage_nymph), base_name, sep="_"); + } else if (!is.null(life_stage_adult)) { + lsi = get_life_stage_index(life_stage, life_stage_adult=life_stage_adult); + file_name = paste(lsi, tolower(life_stage_adult), base_name, sep="_"); + } else { + lsi = get_life_stage_index(life_stage); + file_name = paste(lsi, base_name, sep="_"); + } + file_path = paste("output_dir", file_name, sep="/"); + return(file_path); +} + get_life_stage_index = function(life_stage, life_stage_nymph=NULL, life_stage_adult=NULL) { # Name collection elements so that they # are displayed in logical order. @@ -346,7 +330,6 @@ } # Read the temperature data into a data frame. temperature_data_frame = parse_input_data(opt$input, opt$num_days); -output_dir = "output_dir"; # Get the date labels for plots. date_labels = get_date_labels(temperature_data_frame, opt$num_days); # All latitude values are the same, so get the value for plots from the first row. @@ -968,9 +951,7 @@ if (life_stage == "Egg") { # Start PDF device driver. dev.new(width=20, height=30); - lsi = get_life_stage_index(life_stage); - file_name = paste(lsi, "egg_pop_by_generation.pdf", sep="_"); - file_path = paste(output_dir, file_name, sep="/"); + file_path = get_file_path(life_stage, "egg_pop_by_generation.pdf") pdf(file=file_path, width=20, height=30, bg="white"); par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); # Egg population size by generation. @@ -984,16 +965,14 @@ for (life_stage_nymph in life_stages_nymph) { # Start PDF device driver. dev.new(width=20, height=30); - lsi = get_life_stage_index(life_stage, life_stage_nymph=life_stage_nymph); - file_name = paste(lsi, tolower(life_stage_nymph), "nymph_pop_by_generation.pdf", sep="_"); - file_path = paste(output_dir, file_name, sep="/"); + file_path = get_file_path(life_stage, "nymph_pop_by_generation.pdf", life_stage_nymph=life_stage_nymph) pdf(file=file_path, width=20, height=30, bg="white"); par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); # Nymph population size by generation. maxval = max(P_nymphs+F1_nymphs+F2_nymphs) + 100; render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval, - opt$replications, life_stage, group=P_nymphs, group_std_error=P_nymphs.std_error, group2=F1_nymphs, group2_std_error=F1_nymphs.std_error, - group3=F2_nymphs, group3_std_error=F2_nymphs.std_error, life_stages_nymph=life_stage_nymph); + opt$replications, life_stage, group=P_nymphs, group_std_error=P_nymphs.std_error, group2=F1_nymphs, group2_std_error=F1_nymphs.std_error, + group3=F2_nymphs, group3_std_error=F2_nymphs.std_error, life_stages_nymph=life_stage_nymph); # Turn off device driver to flush output. dev.off(); } @@ -1001,9 +980,7 @@ for (life_stage_adult in life_stages_adult) { # Start PDF device driver. dev.new(width=20, height=30); - lsi = get_life_stage_index(life_stage, life_stage_adult=life_stage_adult); - file_name = paste(lsi, tolower(life_stage_adult), "adult_pop_by_generation.pdf", sep="_"); - file_path = paste(output_dir, file_name, sep="/"); + file_path = get_file_path(life_stage, "adult_pop_by_generation.pdf", life_stage_adult=life_stage_adult) pdf(file=file_path, width=20, height=30, bg="white"); par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); # Adult population size by generation. @@ -1019,9 +996,7 @@ # Name collection elements so that they # are displayed in logical order. dev.new(width=20, height=30); - lsi = get_life_stage_index(life_stage); - file_name = paste(lsi, "total_pop_by_generation.pdf", sep="_"); - file_path = paste(output_dir, file_name, sep="/"); + file_path = get_file_path(life_stage, "total_pop_by_generation.pdf") pdf(file=file_path, width=20, height=30, bg="white"); par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); # Total population size by generation. @@ -1037,9 +1012,7 @@ if (life_stage == "Egg") { # Start PDF device driver. dev.new(width=20, height=30); - lsi = get_life_stage_index(life_stage); - file_name = paste(lsi, "egg_pop.pdf", sep="_"); - file_path = paste(output_dir, file_name, sep="/"); + file_path = get_file_path(life_stage, "egg_pop.pdf") pdf(file=file_path, width=20, height=30, bg="white"); par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); # Egg population size. @@ -1052,9 +1025,7 @@ for (life_stage_nymph in life_stages_nymph) { # Start PDF device driver. dev.new(width=20, height=30); - lsi = get_life_stage_index(life_stage, life_stage_nymph=life_stage_nymph); - file_name = paste(lsi, tolower(life_stage_nymph), "nymph_pop.pdf", sep="_"); - file_path = paste(output_dir, file_name, sep="/"); + file_path = get_file_path(life_stage, "nymph_pop.pdf", life_stage_nymph=life_stage_nymph) pdf(file=file_path, width=20, height=30, bg="white"); par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); if (life_stage_nymph=="Total") { @@ -1080,9 +1051,7 @@ for (life_stage_adult in life_stages_adult) { # Start PDF device driver. dev.new(width=20, height=30); - lsi = get_life_stage_index(life_stage, life_stage_adult=life_stage_adult); - file_name = paste(lsi, tolower(life_stage_adult), "adult_pop.pdf", sep="_"); - file_path = paste(output_dir, file_name, sep="/"); + file_path = get_file_path(life_stage, "adult_pop.pdf", life_stage_adult=life_stage_adult) pdf(file=file_path, width=20, height=30, bg="white"); par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); if (life_stage_adult=="Total") { @@ -1111,9 +1080,7 @@ } else if (life_stage == "Total") { # Start PDF device driver. dev.new(width=20, height=30); - lsi = get_life_stage_index(life_stage); - file_name = paste(lsi, "total_pop.pdf", sep="_"); - file_path = paste(output_dir, file_name, sep="/"); + file_path = get_file_path(life_stage, "total_pop.pdf") pdf(file=file_path, width=20, height=30, bg="white"); par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); # Total population size.