| Previous changeset 22:58255c06d24b (2018-03-08) Next changeset 24:b90f9b781a77 (2018-03-08) |
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insect_phenology_model.R |
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| diff -r 58255c06d24b -r 36d7bb034285 insect_phenology_model.R --- a/insect_phenology_model.R Thu Mar 08 13:28:53 2018 -0500 +++ b/insect_phenology_model.R Thu Mar 08 13:29:02 2018 -0500 |
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| b'@@ -361,8 +361,8 @@\n process_old_nymphs = FALSE;\n process_total_nymphs = FALSE;\n process_adults = FALSE;\n-process_previtellogenic_adults = FALSE;\n-process_vitellogenic_adults = FALSE;\n+process_previttelogenic_adults = FALSE;\n+process_vittelogenic_adults = FALSE;\n process_diapausing_adults = FALSE;\n process_total_adults = FALSE;\n for (life_stage in life_stages) {\n@@ -382,7 +382,7 @@\n # Split life_stages_nymph into a list of strings for plots.\n life_stages_nymph_str = as.character(opt$life_stages_nymph);\n life_stages_nymph = strsplit(life_stages_nymph_str, ",")[[1]];\n- for (life_stage_nymph in opt$life_stages_nymph) {\n+ for (life_stage_nymph in life_stages_nymph) {\n if (life_stage_nymph=="Young") {\n process_young_nymphs = TRUE;\n } else if (life_stage_nymph=="Old") {\n@@ -396,11 +396,11 @@\n # Split life_stages_adult into a list of strings for plots.\n life_stages_adult_str = as.character(opt$life_stages_adult);\n life_stages_adult = strsplit(life_stages_adult_str, ",")[[1]];\n- for (life_stage_adult in opt$life_stages_adult) {\n- if (life_stage_adult=="Previtellogenic") {\n- process_previtellogenic_adults = TRUE;\n- } else if (life_stage_adult=="Vitellogenic") {\n- process_vitellogenic_adults = TRUE;\n+ for (life_stage_adult in life_stages_adult) {\n+ if (life_stage_adult=="Pre-vittelogenic") {\n+ process_previttelogenic_adults = TRUE;\n+ } else if (life_stage_adult=="Vitelogenic") {\n+ process_vittelogenic_adults = TRUE;\n } else if (life_stage_adult=="Diapausing") {\n process_diapausing_adults = TRUE;\n } else if (life_stage_adult=="Total") {\n@@ -408,20 +408,23 @@\n }\n }\n }\n-\n # Initialize matrices.\n if (process_eggs) {\n Eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);\n }\n-if (process_young_nymphs==TRUE | process_total_nymphs==TRUE) {\n+if (process_young_nymphs | process_total_nymphs) {\n YoungNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);\n }\n-if (process_old_nymphs==TRUE | process_total_nymphs==TRUE) {\n+if (process_old_nymphs | process_total_nymphs) {\n OldNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);\n }\n-if (process_adults) {\n- Previtellogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);\n- Vitellogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);\n+if (process_previttelogenic_adults | process_total_adults) {\n+ Previttelogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);\n+}\n+if (process_vittelogenic_adults | process_total_adults) {\n+ Vitelogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);\n+}\n+if (process_diapausing_adults | process_total_adults) {\n Diapausing.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);\n }\n newborn.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);\n@@ -454,10 +457,25 @@\n F1_total_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);\n F2_total_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);\n }\n- if (process_adults) {\n- P_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);\n- F1_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);\n- F2_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);\n+ if (process_previttelogenic_adults) {\n+ P_previttelogenic_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications);\n+ F1_previttelogenic_adults.replications = matrix(rep(0, opt$num_days*opt$replica'..b'_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+ F1_total_adults = m_se[[3]];\n+ F1_total_adults.std_error = m_se[[4]];\n+ F2_total_adults = m_se[[5]];\n+ F2_total_adults.std_error = m_se[[6]];\n }\n }\n \n@@ -1119,11 +1245,46 @@\n file_path = get_file_path(life_stage, "adult_pop_by_generation.pdf", life_stage_adult=life_stage_adult)\n pdf(file=file_path, width=20, height=30, bg="white");\n par(mar=c(5, 6, 4, 4), mfrow=c(3, 1));\n- # Adult population size by generation.\n- maxval = max(P_adults+F1_adults+F2_adults) + 100;\n+ if (life_stage_adult=="Pre-vittelogenic") {\n+ # Pre-vittelogenic adult population size by generation.\n+ maxval = max(P_previttelogenic_adults+F1_previttelogenic_adults+F2_previttelogenic_adults) + 100;\n+ group = P_previttelogenic_adults;\n+ group_std_error = P_previttelogenic_adults.std_error;\n+ group2 = F1_previttelogenic_adults;\n+ group2_std_error = F1_previttelogenic_adults.std_error;\n+ group3 = F2_previttelogenic_adults;\n+ group3_std_error = F2_previttelogenic_adults.std_error;\n+ } else if (life_stage_adult=="Vittelogenic") {\n+ # Vittelogenic adult population size by generation.\n+ maxval = max(P_vittelogenic_adults+F1_vittelogenic_adults+F2_vittelogenic_adults) + 100;\n+ group = P_vittelogenic_adults;\n+ group_std_error = P_vittelogenic_adults.std_error;\n+ group2 = F1_vittelogenic_adults;\n+ group2_std_error = F1_vittelogenic_adults.std_error;\n+ group3 = F2_vittelogenic_adults;\n+ group3_std_error = F2_vittelogenic_adults.std_error;\n+ } else if (life_stage_adult=="Diapausing") {\n+ # Diapausing adult population size by generation.\n+ maxval = max(P_diapausing_adults+F1_diapausing_adults+F2_diapausing_adults) + 100;\n+ group = P_diapausing_adults;\n+ group_std_error = P_diapausing_adults.std_error;\n+ group2 = F1_diapausing_adults;\n+ group2_std_error = F1_diapausing_adults.std_error;\n+ group3 = F2_diapausing_adults;\n+ group3_std_error = F2_diapausing_adults.std_error;\n+ } else if (life_stage_adult=="Total") {\n+ # Total adult population size by generation.\n+ maxval = max(P_total_adults+F1_total_adults+F2_total_adults) + 100;\n+ group = P_total_adults;\n+ group_std_error = P_total_adults.std_error;\n+ group2 = F1_total_adults;\n+ group2_std_error = F1_total_adults.std_error;\n+ group3 = F2_total_adults;\n+ group3_std_error = F2_total_adults.std_error;\n+ }\n render_chart(date_labels, "pop_size_by_generation", opt$plot_std_error, opt$insect, opt$location, latitude, start_date, end_date, days, maxval,\n- opt$replications, life_stage, group=P_adults, group_std_error=P_adults.std_error, group2=F1_adults, group2_std_error=F1_adults.std_error,\n- group3=F2_adults, group3_std_error=F2_adults.std_error, life_stages_adult=life_stage_adult);\n+ opt$replications, life_stage, group=group, group_std_error=group_std_error, group2=group2, group2_std_error=group2_std_error,\n+ group3=group3, group3_std_error=group3_std_error, life_stages_adult=life_stage_adult);\n # Turn off device driver to flush output.\n dev.off();\n }\n' |