Mercurial > repos > greg > insect_phenology_model
changeset 45:315c5e1bc44a draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 23 Apr 2018 10:19:06 -0400 |
| parents | c61d3d9d44db |
| children | 0791cca1fc5c |
| files | insect_phenology_model.R |
| diffstat | 1 files changed, 17 insertions(+), 12 deletions(-) [+] |
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--- a/insect_phenology_model.R Mon Apr 23 10:18:59 2018 -0400 +++ b/insect_phenology_model.R Mon Apr 23 10:19:06 2018 -0400 @@ -13,7 +13,7 @@ make_option(c("--life_stages"), action="store", dest="life_stages", help="Selected life stages for plotting"), make_option(c("--life_stages_adult"), action="store", dest="life_stages_adult", default=NULL, help="Adult life stages for plotting"), make_option(c("--life_stages_nymph"), action="store", dest="life_stages_nymph", default=NULL, help="Nymph life stages for plotting"), - make_option(c("--location"), action="store", dest="location", help="Selected location"), + make_option(c("--location"), action="store", dest="location", default=NULL, help="Selected location"), make_option(c("--min_clutch_size"), action="store", dest="min_clutch_size", type="integer", help="Adjustment of minimum clutch size"), make_option(c("--max_clutch_size"), action="store", dest="max_clutch_size", type="integer", help="Adjustment of maximum clutch size"), make_option(c("--num_days_ytd"), action="store", dest="num_days_ytd", default=NULL, type="integer", help="Total number of days in the year-to-date temperature dataset"), @@ -353,7 +353,7 @@ return(mortality.probability); } -parse_input_data = function(input_ytd, input_norm, num_days_ytd) { +parse_input_data = function(input_ytd, input_norm, num_days_ytd, location) { if (is.null(input_ytd)) { # We're analysing only the 30 year normals data, so create an empty # data frame for containing temperature data after it is converted @@ -401,6 +401,10 @@ if (!is_leap_year) { norm_data_frame = norm_data_frame[-c(60),]; } + # Set the location to be the station name if the user elected no to enter it. + if (is.null(location)) { + location = norm_data_frame$NAME[1]; + } if (is.null(input_ytd)) { # Convert the 30 year normals data to the year-to-date format. for (i in 1:total_days) { @@ -428,7 +432,7 @@ } # Add a column containing the daylight length for each day. temperature_data_frame = add_daylight_length(temperature_data_frame, total_days); - return(list(temperature_data_frame, start_date, end_date, start_doy_ytd, end_doy_ytd, is_leap_year, total_days)); + return(list(temperature_data_frame, start_date, end_date, start_doy_ytd, end_doy_ytd, is_leap_year, total_days, location)); } render_chart = function(ticks, date_labels, chart_type, plot_std_error, insect, location, latitude, start_date, end_date, days, maxval, @@ -525,7 +529,7 @@ cat("Year-to-date number of days: ", opt$num_days_ytd, "\n"); # Parse the inputs. -data_list = parse_input_data(opt$input_ytd, opt$input_norm, opt$num_days_ytd); +data_list = parse_input_data(opt$input_ytd, opt$input_norm, opt$num_days_ytd, opt$location); temperature_data_frame = data_list[[1]]; # Information needed for plots. start_date = data_list[[2]]; @@ -535,6 +539,7 @@ is_leap_year = data_list[[6]]; total_days = data_list[[7]]; total_days_vector = c(1:total_days); +location = data_list[[8]]; # Create copies of the temperature data for generations P, F1 and F2 if we're plotting generations separately. if (plot_generations_separately) { @@ -1464,7 +1469,7 @@ par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); # Egg population size by generation. maxval = max(P_eggs+F1_eggs+F2_eggs) + 100; - render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, + render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, location, latitude, start_date, end_date, total_days_vector, maxval, opt$replications, life_stage, group=P_eggs, group_std_error=P_eggs.std_error, group2=F1_eggs, group2_std_error=F1_eggs.std_error, group3=F2_eggs, group3_std_error=F2_eggs.std_error); # Turn off device driver to flush output. @@ -1504,7 +1509,7 @@ group3 = F2_total_nymphs; group3_std_error = F2_total_nymphs.std_error; } - render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, + render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, location, latitude, start_date, end_date, total_days_vector, maxval, opt$replications, life_stage, group=group, group_std_error=group_std_error, group2=group2, group2_std_error=group2_std_error, group3=group3, group3_std_error=group3_std_error, life_stages_nymph=life_stage_nymph); # Turn off device driver to flush output. @@ -1554,7 +1559,7 @@ group3 = F2_total_adults; group3_std_error = F2_total_adults.std_error; } - render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, + render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, location, latitude, start_date, end_date, total_days_vector, maxval, opt$replications, life_stage, group=group, group_std_error=group_std_error, group2=group2, group2_std_error=group2_std_error, group3=group3, group3_std_error=group3_std_error, life_stages_adult=life_stage_adult); # Turn off device driver to flush output. @@ -1570,7 +1575,7 @@ par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); # Total population size by generation. maxval = max(P+F1+F2) + 100; - render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, + render_chart(ticks, date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, location, latitude, start_date, end_date, total_days_vector, maxval, opt$replications, life_stage, group=P, group_std_error=P.std_error, group2=F1, group2_std_error=F1.std_error, group3=F2, group3_std_error=F2.std_error); # Turn off device driver to flush output. @@ -1587,7 +1592,7 @@ par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); # Egg population size. maxval = max(eggs+eggs.std_error) + 100; - render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, + render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, location, latitude, start_date, end_date, total_days_vector, maxval, opt$replications, life_stage, group=eggs, group_std_error=eggs.std_error); # Turn off device driver to flush output. dev.off(); @@ -1612,7 +1617,7 @@ group_std_error = old_nymphs.std_error; } maxval = max(group+group_std_error) + 100; - render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, + render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, location, latitude, start_date, end_date, total_days_vector, maxval, opt$replications, life_stage, group=group, group_std_error=group_std_error, life_stages_nymph=life_stage_nymph); # Turn off device driver to flush output. @@ -1643,7 +1648,7 @@ group_std_error = diapausing_adults.std_error } maxval = max(group+group_std_error) + 100; - render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, + render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, location, latitude, start_date, end_date, total_days_vector, maxval, opt$replications, life_stage, group=group, group_std_error=group_std_error, life_stages_adult=life_stage_adult); # Turn off device driver to flush output. @@ -1657,7 +1662,7 @@ par(mar=c(5, 6, 4, 4), mfrow=c(3, 1)); # Total population size. maxval = max(eggs+eggs.std_error, total_nymphs+total_nymphs.std_error, total_adults+total_adults.std_error) + 100; - render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, opt$location, latitude, + render_chart(ticks, date_labels, "pop_size_by_life_stage", opt$plot_std_error, opt$insect, location, latitude, start_date, end_date, total_days_vector, maxval, opt$replications, life_stage, group=total_adults, group_std_error=total_adults.std_error, group2=total_nymphs, group2_std_error=total_nymphs.std_error, group3=eggs, group3_std_error=eggs.std_error); # Turn off device driver to flush output.