Mercurial > repos > greg > insect_phenology_model
changeset 23:36d7bb034285 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 08 Mar 2018 13:29:02 -0500 |
| parents | 58255c06d24b |
| children | b90f9b781a77 |
| files | insect_phenology_model.R |
| diffstat | 1 files changed, 246 insertions(+), 85 deletions(-) [+] |
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line diff
--- 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 @@ -361,8 +361,8 @@ process_old_nymphs = FALSE; process_total_nymphs = FALSE; process_adults = FALSE; -process_previtellogenic_adults = FALSE; -process_vitellogenic_adults = FALSE; +process_previttelogenic_adults = FALSE; +process_vittelogenic_adults = FALSE; process_diapausing_adults = FALSE; process_total_adults = FALSE; for (life_stage in life_stages) { @@ -382,7 +382,7 @@ # Split life_stages_nymph into a list of strings for plots. life_stages_nymph_str = as.character(opt$life_stages_nymph); life_stages_nymph = strsplit(life_stages_nymph_str, ",")[[1]]; - for (life_stage_nymph in opt$life_stages_nymph) { + for (life_stage_nymph in life_stages_nymph) { if (life_stage_nymph=="Young") { process_young_nymphs = TRUE; } else if (life_stage_nymph=="Old") { @@ -396,11 +396,11 @@ # Split life_stages_adult into a list of strings for plots. life_stages_adult_str = as.character(opt$life_stages_adult); life_stages_adult = strsplit(life_stages_adult_str, ",")[[1]]; - for (life_stage_adult in opt$life_stages_adult) { - if (life_stage_adult=="Previtellogenic") { - process_previtellogenic_adults = TRUE; - } else if (life_stage_adult=="Vitellogenic") { - process_vitellogenic_adults = TRUE; + for (life_stage_adult in life_stages_adult) { + if (life_stage_adult=="Pre-vittelogenic") { + process_previttelogenic_adults = TRUE; + } else if (life_stage_adult=="Vitelogenic") { + process_vittelogenic_adults = TRUE; } else if (life_stage_adult=="Diapausing") { process_diapausing_adults = TRUE; } else if (life_stage_adult=="Total") { @@ -408,20 +408,23 @@ } } } - # Initialize matrices. if (process_eggs) { Eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); } -if (process_young_nymphs==TRUE | process_total_nymphs==TRUE) { +if (process_young_nymphs | process_total_nymphs) { YoungNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); } -if (process_old_nymphs==TRUE | process_total_nymphs==TRUE) { +if (process_old_nymphs | process_total_nymphs) { OldNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); } -if (process_adults) { - Previtellogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); - Vitellogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); +if (process_previttelogenic_adults | process_total_adults) { + Previttelogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); +} +if (process_vittelogenic_adults | process_total_adults) { + Vitelogenic.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); +} +if (process_diapausing_adults | process_total_adults) { Diapausing.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); } newborn.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); @@ -454,10 +457,25 @@ F1_total_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); F2_total_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); } - if (process_adults) { - P_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); - F1_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); - F2_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + if (process_previttelogenic_adults) { + P_previttelogenic_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + F1_previttelogenic_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + F2_previttelogenic_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + } + if (process_vittelogenic_adults) { + P_vittelogenic_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + F1_vittelogenic_adults = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + F2_vittelogenic_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + } + if (process_diapausing_adults) { + P_diapausing_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + F1_diapausing_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + F2_diapausing_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + } + if (process_total_adults) { + P_total_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + F1_total_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + F2_total_adults.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); } } # Total population. @@ -480,13 +498,19 @@ if (process_eggs) { Eggs = rep(0, opt$num_days); } - if (process_nymphs) { + if (process_young_nymphs | process_total_nymphs) { YoungNymphs = rep(0, opt$num_days); + } + if (process_old_nymphs | process_total_nymphs) { OldNymphs = rep(0, opt$num_days); } - if (process_adults) { - Previtellogenic = rep(0, opt$num_days); - Vitellogenic = rep(0, opt$num_days); + if (process_previttelogenic_adults | process_total_adults) { + Previttelogenic = rep(0, opt$num_days); + } + if (process_vittelogenic_adults | process_total_adults) { + Vitelogenic = rep(0, opt$num_days); + } + if (process_diapausing_adults | process_total_adults) { Diapausing = rep(0, opt$num_days); } N.newborn = rep(0, opt$num_days); @@ -519,10 +543,25 @@ F1.total_nymph = rep(0, opt$num_days); F2.total_nymph = rep(0, opt$num_days); } - if (process_adults) { - P.adult = rep(0, opt$num_days); - F1.adult = rep(0, opt$num_days); - F2.adult = rep(0, opt$num_days); + if (process_previttelogenic_adults) { + P.previttelogenic_adult = rep(0, opt$num_days); + F1.previttelogenic_adult = rep(0, opt$num_days); + F2.previttelogenic_adult = rep(0, opt$num_days); + } + if (process_vittelogenic_adults) { + P.vittelogenic_adult = rep(0, opt$num_days); + F1.vittelogenic_adult = rep(0, opt$num_days); + F2.vittelogenic_adult = rep(0, opt$num_days); + } + if (process_diapausing_adults) { + P.diapausing_adult = rep(0, opt$num_days); + F1.diapausing_adult = rep(0, opt$num_days); + F2.diapausing_adult = rep(0, opt$num_days); + } + if (process_total_adults) { + P.total_adult = rep(0, opt$num_days); + F1.total_adult = rep(0, opt$num_days); + F2.total_adult = rep(0, opt$num_days); } } total.population = NULL; @@ -761,19 +800,23 @@ # For egg population size, column 2 (Stage), must be 0. Eggs[row] = sum(vector.matrix[,2]==0); } - if (process_young_nymphs) { + if (process_young_nymphs | process_total_nymphs) { # For young nymph population size, column 2 (Stage) must be 1. YoungNymphs[row] = sum(vector.matrix[,2]==1); } - if (process_old_nymphs) { + if (process_old_nymphs | process_total_nymphs) { # For old nymph population size, column 2 (Stage) must be 2. OldNymphs[row] = sum(vector.matrix[,2]==2); } - if (process_adults) { - # For pre-vitellogenic population size, column 2 (Stage) must be 3. - Previtellogenic[row] = sum(vector.matrix[,2]==3); - # For vitellogenic population size, column 2 (Stage) must be 4. - Vitellogenic[row] = sum(vector.matrix[,2]==4); + if (process_previttelogenic_adults | process_total_adults) { + # For pre-vittelogenic population size, column 2 (Stage) must be 3. + Previttelogenic[row] = sum(vector.matrix[,2]==3); + } + if (process_vittelogenic_adults | process_total_adults) { + # For vittelogenic population size, column 2 (Stage) must be 4. + Vitelogenic[row] = sum(vector.matrix[,2]==4); + } + if (process_diapausing_adults | process_total_adults) { # For diapausing population size, column 2 (Stage) must be 5. Diapausing[row] = sum(vector.matrix[,2]==5); } @@ -854,25 +897,67 @@ # - column 1 (Generation) is 2 and column 2 (Stage) is 2 (Old nymph) F2.total_nymph[row] = sum((vector.matrix[,1]==2 & vector.matrix[,2]==1) | (vector.matrix[,1]==2 & vector.matrix[,2]==2)); } - if (process_adults) { - # For adult life stage of generation P population - # size, one of the following combinations is required: - # - column 1 (Generation) is 0 and column 2 (Stage) is 3 (Pre-vitellogenic) - # - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vitellogenic) + if (process_previttelogenic_adults) { + # For previttelogenic adult life stage of generation P population + # size, the following combination is required: + # - column 1 (Generation) is 0 and column 2 (Stage) is 3 (Pre-vittelogenic) + P.previttelogenic_adult[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==3); + # For previttelogenic adult life stage of generation F1 population + # size, the following combination is required: + # - column 1 (Generation) is 1 and column 2 (Stage) is 3 (Pre-vittelogenic) + F1.previttelogenic_adult[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==3); + # For previttelogenic adult life stage of generation F2 population + # size, the following combination is required: + # - column 1 (Generation) is 2 and column 2 (Stage) is 3 (Pre-vittelogenic) + F2.previttelogenic_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==3); + } + if (process_vittelogenic_adults) { + # For vittelogenic adult life stage of generation P population + # size, the following combination is required: + # - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vitelogenic) + P.vittelogenic_adult[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==4); + # For vittelogenic adult life stage of generation F1 population + # size, the following combination is required: + # - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vitelogenic) + F1.vittelogenic_adult[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==4); + # For vittelogenic adult life stage of generation F2 population + # size, the following combination is required: + # - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vitelogenic) + F2.vittelogenic_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==4); + } + if (process_diapausing_adults) { + # For diapausing adult life stage of generation P population + # size, the following combination is required: # - column 1 (Generation) is 0 and column 2 (Stage) is 5 (Diapausing) - P.adult[row] = sum((vector.matrix[,1]==0 & vector.matrix[,2]==3) | (vector.matrix[,1]==0 & vector.matrix[,2]==4) | (vector.matrix[,1]==0 & vector.matrix[,2]==5)); - # For adult life stage of generation F1 population + P.diapausing_adult[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==5); + # For diapausing adult life stage of generation F1 population + # size, the following combination is required: + # - column 1 (Generation) is 1 and column 2 (Stage) is 5 (Diapausing) + F1.diapausing_adult[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==5); + # For diapausing adult life stage of generation F2 population + # size, the following combination is required: + # - column 1 (Generation) is 2 and column 2 (Stage) is 5 (Diapausing) + F2.diapausing_adult[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==5); + } + if (process_total_adults) { + # For total adult life stage of generation P population # size, one of the following combinations is required: - # - column 1 (Generation) is 1 and column 2 (Stage) is 3 (Pre-vitellogenic) - # - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vitellogenic) + # - column 1 (Generation) is 0 and column 2 (Stage) is 3 (Pre-vittelogenic) + # - column 1 (Generation) is 0 and column 2 (Stage) is 4 (Vitelogenic) + # - column 1 (Generation) is 0 and column 2 (Stage) is 5 (Diapausing) + P.total_adult[row] = sum((vector.matrix[,1]==0 & vector.matrix[,2]==3) | (vector.matrix[,1]==0 & vector.matrix[,2]==4) | (vector.matrix[,1]==0 & vector.matrix[,2]==5)); + # For total adult life stage of generation F1 population + # size, one of the following combinations is required: + # - column 1 (Generation) is 1 and column 2 (Stage) is 3 (Pre-vittelogenic) + # - column 1 (Generation) is 1 and column 2 (Stage) is 4 (Vitelogenic) # - column 1 (Generation) is 1 and column 2 (Stage) is 5 (Diapausing) - F1.adult[row] = sum((vector.matrix[,1]==1 & vector.matrix[,2]==3) | (vector.matrix[,1]==1 & vector.matrix[,2]==4) | (vector.matrix[,1]==1 & vector.matrix[,2]==5)); - # For adult life stage of generation F2 population + F1.total_adult[row] = sum((vector.matrix[,1]==1 & vector.matrix[,2]==3) | (vector.matrix[,1]==1 & vector.matrix[,2]==4) | (vector.matrix[,1]==1 & vector.matrix[,2]==5)); + # For total adult life stage of generation F2 population # size, one of the following combinations is required: - # - column 1 (Generation) is 2 and column 2 (Stage) is 3 (Pre-vitellogenic) - # - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vitellogenic) + # - column 1 (Generation) is 2 and column 2 (Stage) is 3 (Pre-vittelogenic) + # - column 1 (Generation) is 2 and column 2 (Stage) is 4 (Vitelogenic) # - column 1 (Generation) is 2 and column 2 (Stage) is 5 (Diapausing) - F2.adult[row] = sum((vector.matrix[,1]==2 & vector.matrix[,2]==3) | (vector.matrix[,1]==2 & vector.matrix[,2]==4) | (vector.matrix[,1]==2 & vector.matrix[,2]==5)); + F2.total_adult[row] = sum((vector.matrix[,1]==2 & vector.matrix[,2]==3) | (vector.matrix[,1]==2 & vector.matrix[,2]==4) | (vector.matrix[,1]==2 & vector.matrix[,2]==5)); } } } # End of days specified in the input temperature data. @@ -883,15 +968,19 @@ if (process_eggs) { Eggs.replications[,current_replication] = Eggs; } - if (process_young_nymphs==TRUE | process_total_nymphs==TRUE) { + if (process_young_nymphs | process_total_nymphs) { YoungNymphs.replications[,current_replication] = YoungNymphs; } - if (process_old_nymphs==TRUE | process_total_nymphs==TRUE) { + if (process_old_nymphs | process_total_nymphs) { OldNymphs.replications[,current_replication] = OldNymphs; } - if (process_adults) { - Previtellogenic.replications[,current_replication] = Previtellogenic; - Vitellogenic.replications[,current_replication] = Vitellogenic; + if (process_previttelogenic_adults | process_total_adults) { + Previttelogenic.replications[,current_replication] = Previttelogenic; + } + if (process_vittelogenic_adults | process_total_adults) { + Vitelogenic.replications[,current_replication] = Vitelogenic; + } + if (process_diapausing_adults | process_total_adults) { Diapausing.replications[,current_replication] = Diapausing; } newborn.replications[,current_replication] = N.newborn; @@ -924,10 +1013,25 @@ F1_total_nymphs.replications[,current_replication] = F1.total_nymph; F2_total_nymphs.replications[,current_replication] = F2.total_nymph; } - if (process_adults) { - P_adults.replications[,current_replication] = P.adult; - F1_adults.replications[,current_replication] = F1.adult; - F2_adults.replications[,current_replication] = F2.adult; + if (process_previttelogenic_adults) { + P_previttelogenic_adults.replications[,current_replication] = P.previttelogenic_adult; + F1_previttelogenic_adults.replications[,current_replication] = F1.previttelogenic_adult; + F2_previttelogenic_adults.replications[,current_replication] = F2.previttelogenic_adult; + } + if (process_vittelogenic_adults) { + P_vittelogenic_adults.replications[,current_replication] = P.vittelogenic_adult; + F1_vittelogenic_adults.replications[,current_replication] = F1.vittelogenic_adult; + F2_vittelogenic_adults.replications[,current_replication] = F2.vittelogenic_adult; + } + if (process_diapausing_adults) { + P_diapausing_adults.replications[,current_replication] = P.diapausing_adult; + F1_diapausing_adults.replications[,current_replication] = F1.diapausing_adult; + F2_diapausing_adults.replications[,current_replication] = F2.diapausing_adult; + } + if (process_total_adults) { + P_total_adults.replications[,current_replication] = P.total_adult; + F1_total_adults.replications[,current_replication] = F1.total_adult; + F2_total_adults.replications[,current_replication] = F2.total_adult; } } population.replications[,current_replication] = total.population; @@ -966,23 +1070,23 @@ for (life_stage_adult in life_stages_adult) { if (life_stage_adult=="Total") { # Mean value for all adults. - total_adults = apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, mean); + total_adults = apply((Previttelogenic.replications+Vitelogenic.replications+Diapausing.replications), 1, mean); # Standard error for all adults. - total_adults.std_error = apply((Previtellogenic.replications+Vitellogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications); + total_adults.std_error = apply((Previttelogenic.replications+Vitelogenic.replications+Diapausing.replications), 1, sd) / sqrt(opt$replications); } else if (life_stage_adult == "Pre-vittelogenic") { - # Mean value for previtellogenic adults. - previttelogenic_adults = apply(Previtellogenic.replications, 1, mean); - # Standard error for previtellogenic adults. - previttelogenic_adults.std_error = apply(Previtellogenic.replications, 1, sd) / sqrt(opt$replications); + # Mean value for previttelogenic adults. + previttelogenic_adults = apply(Previttelogenic.replications, 1, mean); + # Standard error for previttelogenic adults. + previttelogenic_adults.std_error = apply(Previttelogenic.replications, 1, sd) / sqrt(opt$replications); } else if (life_stage_adult == "Vittelogenic") { - # Mean value for vitellogenic adults. - vittelogenic_adults = apply(Vitellogenic.replications, 1, mean); - # Standard error for vitellogenic adults. - vittelogenic_adults.std_error = apply(Vitellogenic.replications, 1, sd) / sqrt(opt$replications); + # Mean value for vittelogenic adults. + vittelogenic_adults = apply(Vitelogenic.replications, 1, mean); + # Standard error for vittelogenic adults. + vittelogenic_adults.std_error = apply(Vitelogenic.replications, 1, sd) / sqrt(opt$replications); } else if (life_stage_adult == "Diapausing") { - # Mean value for vitellogenic adults. + # Mean value for vittelogenic adults. diapausing_adults = apply(Diapausing.replications, 1, mean); - # Standard error for vitellogenic adults. + # Standard error for vittelogenic adults. diapausing_adults.std_error = apply(Diapausing.replications, 1, sd) / sqrt(opt$replications); } } @@ -1032,19 +1136,41 @@ F2_total_nymphs = m_se[[5]]; F2_total_nymphs.std_error = m_se[[6]]; } - if (process_adults) { - # Mean value for P_adults. - P_adults = apply(P_adults.replications, 1, mean); - # Standard error for P_adults. - P_adults.std_error = apply(P_adults.replications, 1, sd) / sqrt(opt$replications); - # Mean value for F1 adults. - F1_adults = apply(F1_adults.replications, 1, mean); - # Standard error for F1_adults. - F1_adults.std_error = apply(F1_adults.replications, 1, sd) / sqrt(opt$replications); - # Mean value for F2_adults. - F2_adults = apply(F2_adults.replications, 1, mean); - # Standard error for F2_adults. - F2_adults.std_error = apply(F2_adults.replications, 1, sd) / sqrt(opt$replications); + if (process_previttelogenic_adults) { + m_se = get_mean_and_std_error(P_previttelogenic_adults.replications, F1_previttelogenic_adults.replications, F2_previttelogenic_adults.replications); + P_previttelogenic_adults = m_se[[1]]; + P_previttelogenic_adults.std_error = m_se[[2]]; + F1_previttelogenic_adults = m_se[[3]]; + F1_previttelogenic_adults.std_error = m_se[[4]]; + F2_previttelogenic_adults = m_se[[5]]; + F2_previttelogenic_adults.std_error = m_se[[6]]; + } + if (process_vittelogenic_adults) { + m_se = get_mean_and_std_error(P_vittelogenic_adults.replications, F1_vittelogenic_adults.replications, F2_vittelogenic_adults.replications); + P_vittelogenic_adults = m_se[[1]]; + P_vittelogenic_adults.std_error = m_se[[2]]; + F1_vittelogenic_adults = m_se[[3]]; + F1_vittelogenic_adults.std_error = m_se[[4]]; + F2_vittelogenic_adults = m_se[[5]]; + F2_vittelogenic_adults.std_error = m_se[[6]]; + } + if (process_diapausing_adults) { + m_se = get_mean_and_std_error(P_diapausing_adults.replications, F1_diapausing_adults.replications, F2_diapausing_adults.replications); + P_diapausing_adults = m_se[[1]]; + P_diapausing_adults.std_error = m_se[[2]]; + F1_diapausing_adults = m_se[[3]]; + F1_diapausing_adults.std_error = m_se[[4]]; + F2_diapausing_adults = m_se[[5]]; + F2_diapausing_adults.std_error = m_se[[6]]; + } + if (process_total_adults) { + m_se = get_mean_and_std_error(P_total_adults.replications, F1_total_adults.replications, F2_total_adults.replications); + P_total_adults = m_se[[1]]; + P_total_adults.std_error = m_se[[2]]; + F1_total_adults = m_se[[3]]; + F1_total_adults.std_error = m_se[[4]]; + F2_total_adults = m_se[[5]]; + F2_total_adults.std_error = m_se[[6]]; } } @@ -1119,11 +1245,46 @@ 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. - maxval = max(P_adults+F1_adults+F2_adults) + 100; + if (life_stage_adult=="Pre-vittelogenic") { + # Pre-vittelogenic adult population size by generation. + maxval = max(P_previttelogenic_adults+F1_previttelogenic_adults+F2_previttelogenic_adults) + 100; + group = P_previttelogenic_adults; + group_std_error = P_previttelogenic_adults.std_error; + group2 = F1_previttelogenic_adults; + group2_std_error = F1_previttelogenic_adults.std_error; + group3 = F2_previttelogenic_adults; + group3_std_error = F2_previttelogenic_adults.std_error; + } else if (life_stage_adult=="Vittelogenic") { + # Vittelogenic adult population size by generation. + maxval = max(P_vittelogenic_adults+F1_vittelogenic_adults+F2_vittelogenic_adults) + 100; + group = P_vittelogenic_adults; + group_std_error = P_vittelogenic_adults.std_error; + group2 = F1_vittelogenic_adults; + group2_std_error = F1_vittelogenic_adults.std_error; + group3 = F2_vittelogenic_adults; + group3_std_error = F2_vittelogenic_adults.std_error; + } else if (life_stage_adult=="Diapausing") { + # Diapausing adult population size by generation. + maxval = max(P_diapausing_adults+F1_diapausing_adults+F2_diapausing_adults) + 100; + group = P_diapausing_adults; + group_std_error = P_diapausing_adults.std_error; + group2 = F1_diapausing_adults; + group2_std_error = F1_diapausing_adults.std_error; + group3 = F2_diapausing_adults; + group3_std_error = F2_diapausing_adults.std_error; + } else if (life_stage_adult=="Total") { + # Total adult population size by generation. + maxval = max(P_total_adults+F1_total_adults+F2_total_adults) + 100; + group = P_total_adults; + group_std_error = P_total_adults.std_error; + group2 = F1_total_adults; + group2_std_error = F1_total_adults.std_error; + group3 = F2_total_adults; + group3_std_error = F2_total_adults.std_error; + } 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_adults, group_std_error=P_adults.std_error, group2=F1_adults, group2_std_error=F1_adults.std_error, - group3=F2_adults, group3_std_error=F2_adults.std_error, life_stages_adult=life_stage_adult); + 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. dev.off(); }