| Previous changeset 30:0e49e1d1c5a1 (2018-03-19) Next changeset 32:94afb3e484c3 (2018-03-19) |
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insect_phenology_model.R |
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| diff -r 0e49e1d1c5a1 -r ef6aa8c21729 insect_phenology_model.R --- a/insect_phenology_model.R Mon Mar 19 10:30:23 2018 -0400 +++ b/insect_phenology_model.R Mon Mar 19 10:30:30 2018 -0400 |
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| b'@@ -18,7 +18,10 @@\n make_option(c("--num_days"), action="store", dest="num_days", type="integer", help="Total number of days in the temperature dataset"),\n make_option(c("--nymph_mortality"), action="store", dest="nymph_mortality", type="integer", help="Adjustment rate for nymph mortality"),\n make_option(c("--old_nymph_accumulation"), action="store", dest="old_nymph_accumulation", type="integer", help="Adjustment of degree-days accumulation (young nymph->old nymph)"),\n- make_option(c("--output"), action="store", dest="output", help="Dataset containing analyzed data"),\n+ make_option(c("--output_combined"), action="store", dest="output_combined", help="Dataset containing analyzed data for combined generations"),\n+ make_option(c("--output_f1"), action="store", dest="output_f1", default=NULL, help="Dataset containing analyzed data for generation F1"),\n+ make_option(c("--output_f2"), action="store", dest="output_f2", default=NULL, help="Dataset containing analyzed data for generation F2"),\n+ make_option(c("--output_p"), action="store", dest="output_p", default=NULL, help="Dataset containing analyzed data for generation P"),\n make_option(c("--oviposition"), action="store", dest="oviposition", type="integer", help="Adjustment for oviposition rate"),\n make_option(c("--photoperiod"), action="store", dest="photoperiod", type="double", help="Critical photoperiod for diapause induction/termination"),\n make_option(c("--plot_generations_separately"), action="store", dest="plot_generations_separately", help="Plot Plot P, F1 and F2 as separate lines or pool across them"),\n@@ -354,6 +357,12 @@\n }\n # Read the temperature data into a data frame.\n temperature_data_frame = parse_input_data(opt$input, opt$num_days);\n+# Create copies of the temperature data for generations P, F1 and F2 if we\'re plotting generations separately.\n+if (plot_generations_separately) {\n+ temperature_data_frame_P = data.frame(temperature_data_frame);\n+ temperature_data_frame_F1 = data.frame(temperature_data_frame);\n+ temperature_data_frame_F2 = data.frame(temperature_data_frame);\n+}\n # Get the date labels for plots.\n date_labels = get_date_labels(temperature_data_frame, opt$num_days);\n # All latitude values are the same, so get the value for plots from the first row.\n@@ -1128,78 +1137,134 @@\n m_se = get_mean_and_std_error(P_eggs.replications, F1_eggs.replications, F2_eggs.replications);\n P_eggs = m_se[[1]];\n P_eggs.std_error = m_se[[2]];\n+ temperature_data_frame_P = append_vector(temperature_data_frame_P, P_eggs, "EGG-P");\n+ temperature_data_frame_P = append_vector(temperature_data_frame_P, P_eggs.std_error, "EGG-P-SE");\n F1_eggs = m_se[[3]];\n F1_eggs.std_error = m_se[[4]];\n+ temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_eggs, "EGG-F1");\n+ temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_eggs.std_error, "EGG-F1-SE");\n F2_eggs = m_se[[5]];\n F2_eggs.std_error = m_se[[6]];\n+ temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_eggs, "EGG-F2");\n+ temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_eggs.std_error, "EGG-F2-SE");\n }\n if (process_young_nymphs) {\n m_se = get_mean_and_std_error(P_young_nymphs.replications, F1_young_nymphs.replications, F2_young_nymphs.replications);\n P_young_nymphs = m_se[[1]];\n P_young_nymphs.std_error = m_se[[2]];\n+ temperature_data_frame_P = append_vector(temperature_data_frame_P, P_young_nymphs, "YOUNGNYMPH-P");\n+ temperature_data_frame_P = append_vector(temperature_data_frame_P, P_young_nymphs.std_error, "YOUNGNYMPH-P-SE");\n F1_young_nymphs = m_se[[3]];\n F1_young_nymphs.std_error = m_se[[4]];\n+ temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_young_nymphs, "YOUNGNYMPH-F1");\n+ temperature_data_frame_F1 = append_vector('..b' temperature_data_frame_P = append_vector(temperature_data_frame_P, P_vittelogenic_adults.std_error, "VITADULT-P-SE");\n F1_vittelogenic_adults = m_se[[3]];\n F1_vittelogenic_adults.std_error = m_se[[4]];\n+ temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_vittelogenic_adults, "VITADULT-F1");\n+ temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_vittelogenic_adults.std_error, "VITADULT-F1-SE");\n F2_vittelogenic_adults = m_se[[5]];\n F2_vittelogenic_adults.std_error = m_se[[6]];\n+ temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_vittelogenic_adults, "VITADULT-F2");\n+ temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_vittelogenic_adults.std_error, "VITADULT-F2-SE");\n }\n if (process_diapausing_adults) {\n m_se = get_mean_and_std_error(P_diapausing_adults.replications, F1_diapausing_adults.replications, F2_diapausing_adults.replications);\n P_diapausing_adults = m_se[[1]];\n P_diapausing_adults.std_error = m_se[[2]];\n+ temperature_data_frame_P = append_vector(temperature_data_frame_P, P_diapausing_adults, "DIAPAUSINGADULT-P");\n+ temperature_data_frame_P = append_vector(temperature_data_frame_P, P_diapausing_adults.std_error, "DIAPAUSINGADULT-P-SE");\n F1_diapausing_adults = m_se[[3]];\n F1_diapausing_adults.std_error = m_se[[4]];\n+ temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_diapausing_adults, "DIAPAUSINGADULT-F1");\n+ temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_diapausing_adults.std_error, "DIAPAUSINGADULT-F1-SE");\n F2_diapausing_adults = m_se[[5]];\n F2_diapausing_adults.std_error = m_se[[6]];\n+ temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_diapausing_adults, "DIAPAUSINGADULT-F2");\n+ temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_diapausing_adults.std_error, "DIAPAUSINGADULT-F2-SE");\n }\n if (process_total_adults) {\n m_se = get_mean_and_std_error(P_total_adults.replications, F1_total_adults.replications, F2_total_adults.replications);\n P_total_adults = m_se[[1]];\n P_total_adults.std_error = m_se[[2]];\n+ temperature_data_frame_P = append_vector(temperature_data_frame_P, P_total_adults, "TOTALADULT-P");\n+ temperature_data_frame_P = append_vector(temperature_data_frame_P, P_total_adults.std_error, "TOTALADULT-P-SE");\n F1_total_adults = m_se[[3]];\n F1_total_adults.std_error = m_se[[4]];\n+ temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_total_adults, "TOTALADULT-F1");\n+ temperature_data_frame_F1 = append_vector(temperature_data_frame_F1, F1_total_adults.std_error, "TOTALADULT-F1-SE");\n F2_total_adults = m_se[[5]];\n F2_total_adults.std_error = m_se[[6]];\n+ temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_adults, "TOTALADULT-F2");\n+ temperature_data_frame_F2 = append_vector(temperature_data_frame_F2, F2_total_adults.std_error, "TOTALADULT-F2-SE");\n }\n }\n \n-# Save the analyzed data.\n-write.csv(temperature_data_frame, file=opt$output, row.names=F);\n+# Save the analyzed data for combined generations.\n+write.csv(temperature_data_frame, file=opt$output_combined, row.names=F);\n+if (plot_generations_separately) {\n+ # Save the analyzed data for generation P.\n+ write.csv(temperature_data_frame_P, file=opt$output_p, row.names=F);\n+ # Save the analyzed data for generation F1.\n+ write.csv(temperature_data_frame_F1, file=opt$output_f1, row.names=F);\n+ # Save the analyzed data for generation F2.\n+ write.csv(temperature_data_frame_F2, file=opt$output_f2, row.names=F);\n+}\n # Display the total number of days in the Galaxy history item blurb.\n cat("Number of days: ", opt$num_days, "\\n");\n # Information needed for plots plots.\n' |