Mercurial > repos > greg > insect_phenology_model
changeset 20:214217142600 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 08 Mar 2018 08:06:18 -0500 |
| parents | 3c6e94e477cb |
| children | 6349699fc9fa |
| files | insect_phenology_model.R |
| diffstat | 1 files changed, 246 insertions(+), 76 deletions(-) [+] |
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--- a/insect_phenology_model.R Tue Mar 06 14:26:45 2018 -0500 +++ b/insect_phenology_model.R Thu Mar 08 08:06:18 2018 -0500 @@ -71,7 +71,6 @@ 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); @@ -116,6 +115,22 @@ return(lsi); } +get_mean_and_std_error = function(p_replications, f1_replications, f2_replications) { + # P mean. + p_m = apply(p_replications, 1, mean); + # P standard error. + p_se = apply(p_replications, 1, sd) / sqrt(opt$replications); + # F1 mean. + f1_m = apply(f1_replications, 1, mean); + # F1 standard error. + f1_se = apply(f1_replications, 1, sd) / sqrt(opt$replications); + # F2 mean. + f2_m = apply(f2_replications, 1, mean); + # F2 standard error. + f2_se = apply(f2_replications, 1, sd) / sqrt(opt$replications); + return(list(p_m, p_se, f1_m, f1_se, f2_m, f2_se)) +} + get_temperature_at_hour = function(latitude, temperature_data_frame, row, num_days) { # Base development threshold for Brown Marmorated Stink Bug # insect phenology model. @@ -237,10 +252,10 @@ return(temperature_data_frame); } - render_chart = function(date_labels, chart_type, plot_std_error, insect, location, latitude, start_date, end_date, days, maxval, - replications, life_stage, group, group_std_error, group2=NULL, group2_std_error=NULL, group3=NULL, group3_std_error=NULL, - life_stages_adult=NULL, life_stages_nymph=NULL) { + replications, life_stage, group, group_std_error, group2=NULL, group2_std_error=NULL, group3=NULL, group3_std_error=NULL, + life_stages_adult=NULL, life_stages_nymph=NULL) { + cat("In render_chart, chart_type: ", chart_type, "\n"); if (chart_type=="pop_size_by_life_stage") { if (life_stage=="Total") { title = paste(insect, ": Reps", replications, ":", life_stage, "Pop :", location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" "); @@ -300,6 +315,10 @@ title_str = paste(":", life_stages_adult, "Adult Pop by Gen", ":", sep=" "); } title = paste(insect, ": Reps", replications, title_str, location, ": Lat", latitude, ":", start_date, "-", end_date, sep=" "); + cat("In render_chart, title: ", title, "\n"); + cat("In render_chart, group: ", group, "\n"); + cat("In render_chart, group2: ", group2, "\n"); + cat("In render_chart, group3: ", group3, "\n"); legend_text = c("P", "F1", "F2"); columns = c(1, 2, 4); plot(days, group, main=title, type="l", ylim=c(0, maxval), axes=F, lwd=2, xlab="", ylab="", cex=3, cex.lab=3, cex.axis=3, cex.main=3); @@ -336,13 +355,21 @@ latitude = temperature_data_frame$LATITUDE[1]; # Get the number of days for plots. num_columns = dim(temperature_data_frame)[2]; +# Determine the specified life stages for processing. # Split life_stages into a list of strings for plots. life_stages_str = as.character(opt$life_stages); life_stages = strsplit(life_stages_str, ",")[[1]]; # Determine the data we need to generate for plotting. process_eggs = FALSE; process_nymphs = FALSE; +process_young_nymphs = FALSE; +process_old_nymphs = FALSE; +process_total_nymphs = FALSE; process_adults = FALSE; +process_previtellogenic_adults = FALSE; +process_vitellogenic_adults = FALSE; +process_diapausing_adults = FALSE; +process_total_adults = FALSE; for (life_stage in life_stages) { if (life_stage=="Total") { process_eggs = TRUE; @@ -356,22 +383,60 @@ process_adults = TRUE; } } +if (process_nymphs) { + # Split life_stages_nymph into a list of strings for plots. + life_stages_nymph_str = as.character(opt$life_stages_nymph); + life_stages_nymph = strsplit(life_stages_nymph_str, ",")[[1]]; + for (life_stage_nymph in opt$life_stages_nymph) { + if (life_stage_nymph=="Young") { + process_young_nymphs = TRUE; + } else if (life_stage_nymph=="Old") { + process_old_nymphs = TRUE; + } else if (life_stage_nymph=="Total") { + process_total_nymphs = TRUE; + } + } +} if (process_adults) { # Split life_stages_adult into a list of strings for plots. life_stages_adult_str = as.character(opt$life_stages_adult); life_stages_adult = strsplit(life_stages_adult_str, ",")[[1]]; + for (life_stage_adult in opt$life_stages_adult) { + if (life_stage_adult=="Previtellogenic") { + process_previtellogenic_adults = TRUE; + } else if (life_stage_adult=="Vitellogenic") { + process_vitellogenic_adults = TRUE; + } else if (life_stage_adult=="Diapausing") { + process_diapausing_adults = TRUE; + } else if (life_stage_adult=="Total") { + process_total_adults = TRUE; + } + } } -if (process_nymphs) { -# Split life_stages_nymph into a list of strings for plots. - life_stages_nymph_str = as.character(opt$life_stages_nymph); - life_stages_nymph = strsplit(life_stages_nymph_str, ",")[[1]]; -} +cat("process_eggs: ", process_eggs, "\n"); +cat("process_nymphs: ", process_nymphs, "\n"); +cat("process_young_nymphs: ", process_young_nymphs, "\n"); +cat("process_old_nymphs: ", process_old_nymphs, "\n"); +cat("process_total_nymphs: ", process_total_nymphs, "\n"); +cat("process_adults: ", process_adults, "\n"); +cat("process_previtellogenic_adults: ", process_previtellogenic_adults, "\n"); +cat("process_vitellogenic_adults: ", process_vitellogenic_adults, "\n"); +cat("process_diapausing_adults: ", process_diapausing_adults, "\n"); +cat("process_total_adults: ", process_total_adults, "\n"); +cat("life_stages: ", life_stages, "\n"); +cat("life_stages_nymph: ", life_stages_nymph, "\n"); +cat("life_stages_adult: ", life_stages_adult, "\n"); + # Initialize matrices. if (process_eggs) { Eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); } -if (process_nymphs) { +cat("process_young_nymphs==TRUE: ", process_young_nymphs==TRUE, "\n"); +cat("process_total_nymphs==TRUE: ", process_total_nymphs==TRUE, "\n"); +if (process_young_nymphs==TRUE | process_total_nymphs==TRUE) { YoungNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); +} +if (process_old_nymphs==TRUE | process_total_nymphs==TRUE) { OldNymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); } if (process_adults) { @@ -394,10 +459,20 @@ F1_eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); F2_eggs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); } - if (process_nymphs) { - P_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); - F1_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); - F2_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + if (process_young_nymphs) { + P_young_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + F1_young_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + F2_young_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + } + if (process_old_nymphs) { + P_old_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + F1_old_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + F2_old_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + } + if (process_total_nymphs) { + P_total_nymphs.replications = matrix(rep(0, opt$num_days*opt$replications), ncol=opt$replications); + F1_total_nymphs.replications = matrix(rep(0, opt$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); @@ -449,10 +524,20 @@ F1.egg = rep(0, opt$num_days); F2.egg = rep(0, opt$num_days); } - if (process_nymphs) { - P.nymph = rep(0, opt$num_days); - F1.nymph = rep(0, opt$num_days); - F2.nymph = rep(0, opt$num_days); + if (process_young_nymphs) { + P.young_nymph = rep(0, opt$num_days); + F1.young_nymph = rep(0, opt$num_days); + F2.young_nymph = rep(0, opt$num_days); + } + if (process_old_nymphs) { + P.old_nymph = rep(0, opt$num_days); + F1.old_nymph = rep(0, opt$num_days); + F2.old_nymph = rep(0, opt$num_days); + } + if (process_total_nymphs) { + P.total_nymph = rep(0, opt$num_days); + 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); @@ -696,9 +781,11 @@ # For egg population size, column 2 (Stage), must be 0. Eggs[row] = sum(vector.matrix[,2]==0); } - if (process_nymphs) { + if (process_young_nymphs) { # For young nymph population size, column 2 (Stage) must be 1. YoungNymphs[row] = sum(vector.matrix[,2]==1); + } + if (process_old_nymphs) { # For old nymph population size, column 2 (Stage) must be 2. OldNymphs[row] = sum(vector.matrix[,2]==2); } @@ -742,22 +829,50 @@ # column 1 (generation) is 2 and column 2 (Stage) is 0. F2.egg[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==0); } - if (process_nymphs) { - # For nymph life stage of generation P population + if (process_young_nymphs) { + # For young nymph life stage of generation P population + # size, the following combination is required: + # - column 1 (Generation) is 0 and column 2 (Stage) is 1 (Young nymph) + P.young_nymph[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==1); + # For young nymph life stage of generation F1 population + # size, the following combination is required: + # - column 1 (Generation) is 1 and column 2 (Stage) is 1 (Young nymph) + F1.young_nymph[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==1); + # For young nymph life stage of generation F2 population + # size, the following combination is required: + # - column 1 (Generation) is 2 and column 2 (Stage) is 1 (Young nymph) + F2.young_nymph[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==1); + } + if (process_old_nymphs) { + # For old nymph life stage of generation P population + # size, the following combination is required: + # - column 1 (Generation) is 0 and column 2 (Stage) is 2 (Old nymph) + P.old_nymph[row] = sum(vector.matrix[,1]==0 & vector.matrix[,2]==2); + # For old nymph life stage of generation F1 population + # size, the following combination is required: + # - column 1 (Generation) is 1 and column 2 (Stage) is 2 (Old nymph) + F1.old_nymph[row] = sum(vector.matrix[,1]==1 & vector.matrix[,2]==2); + # For old nymph life stage of generation F2 population + # size, the following combination is required: + # - column 1 (Generation) is 2 and column 2 (Stage) is 2 (Old nymph) + F2.old_nymph[row] = sum(vector.matrix[,1]==2 & vector.matrix[,2]==2); + } + if (process_total_nymphs) { + # For total nymph life stage of generation P population # size, one of the following combinations is required: # - column 1 (Generation) is 0 and column 2 (Stage) is 1 (Young nymph) # - column 1 (Generation) is 0 and column 2 (Stage) is 2 (Old nymph) - P.nymph[row] = sum((vector.matrix[,1]==0 & vector.matrix[,2]==1) | (vector.matrix[,1]==0 & vector.matrix[,2]==2)); - # For nymph life stage of generation F1 population + P.total_nymph[row] = sum((vector.matrix[,1]==0 & vector.matrix[,2]==1) | (vector.matrix[,1]==0 & vector.matrix[,2]==2)); + # For total nymph life stage of generation F1 population # size, one of the following combinations is required: # - column 1 (Generation) is 1 and column 2 (Stage) is 1 (Young nymph) # - column 1 (Generation) is 1 and column 2 (Stage) is 2 (Old nymph) - F1.nymph[row] = sum((vector.matrix[,1]==1 & vector.matrix[,2]==1) | (vector.matrix[,1]==1 & vector.matrix[,2]==2)); - # For nymph life stage of generation F2 population + F1.total_nymph[row] = sum((vector.matrix[,1]==1 & vector.matrix[,2]==1) | (vector.matrix[,1]==1 & vector.matrix[,2]==2)); + # For total nymph life stage of generation F2 population # size, one of the following combinations is required: # - column 1 (Generation) is 2 and column 2 (Stage) is 1 (Young nymph) # - column 1 (Generation) is 2 and column 2 (Stage) is 2 (Old nymph) - F2.nymph[row] = sum((vector.matrix[,1]==2 & vector.matrix[,2]==1) | (vector.matrix[,1]==2 & vector.matrix[,2]==2)); + 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 @@ -788,8 +903,10 @@ if (process_eggs) { Eggs.replications[,current_replication] = Eggs; } - if (process_nymphs) { + if (process_young_nymphs==TRUE | process_total_nymphs==TRUE) { YoungNymphs.replications[,current_replication] = YoungNymphs; + } + if (process_old_nymphs==TRUE | process_total_nymphs==TRUE) { OldNymphs.replications[,current_replication] = OldNymphs; } if (process_adults) { @@ -812,10 +929,20 @@ F1_eggs.replications[,current_replication] = F1.egg; F2_eggs.replications[,current_replication] = F2.egg; } - if (process_nymphs) { - P_nymphs.replications[,current_replication] = P.nymph; - F1_nymphs.replications[,current_replication] = F1.nymph; - F2_nymphs.replications[,current_replication] = F2.nymph; + if (process_young_nymphs) { + P_young_nymphs.replications[,current_replication] = P.young_nymph; + F1_young_nymphs.replications[,current_replication] = F1.young_nymph; + F2_young_nymphs.replications[,current_replication] = F2.young_nymph; + } + if (process_old_nymphs) { + P_old_nymphs.replications[,current_replication] = P.old_nymph; + F1_old_nymphs.replications[,current_replication] = F1.old_nymph; + F2_old_nymphs.replications[,current_replication] = F2.old_nymph; + } + if (process_total_nymphs) { + P_total_nymphs.replications[,current_replication] = P.total_nymph; + 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; @@ -882,58 +1009,61 @@ } if (plot_generations_separately) { - # Mean value for P which is Parental, or overwintered adults. - P = apply(P.replications, 1, mean); - # Standard error for P. - P.std_error = apply(P.replications, 1, sd) / sqrt(opt$replications); - # Mean value for F1, which is the first field-produced generation. - F1 = apply(F1.replications, 1, mean); - # Standard error for F1. - F1.std_error = apply(F1.replications, 1, sd) / sqrt(opt$replications); - # Mean value for F2, which is the second field-produced generation. - F2 = apply(F2.replications, 1, mean); - # Standard error for F2. - F2.std_error = apply(F2.replications, 1, sd) / sqrt(opt$replications); + m_se = get_mean_and_std_error(P.replications, F1.replications, F2.replications); + P = m_se[[1]]; + P.std_error = m_se[[2]]; + F1 = m_se[[3]]; + F1.std_error = m_se[[4]]; + F2 = m_se[[5]]; + F2.std_error = m_se[[6]]; if (process_eggs) { - # Mean value for P eggs. - P_eggs = apply(P_eggs.replications, 1, mean); - # Standard error for P_eggs. - P_eggs.std_error = apply(P_eggs.replications, 1, sd) / sqrt(opt$replications); - # Mean value for F1 eggs. - F1_eggs = apply(F1_eggs.replications, 1, mean); - # Standard error for F1 eggs. - F1_eggs.std_error = apply(F1_eggs.replications, 1, sd) / sqrt(opt$replications); - # Mean value for F2 eggs. - F2_eggs = apply(F2_eggs.replications, 1, mean); - # Standard error for F2 eggs. - F2_eggs.std_error = apply(F2_eggs.replications, 1, sd) / sqrt(opt$replications); + m_se = get_mean_and_std_error(P_eggs.replications, F1_eggs.replications, F2_eggs.replications); + P_eggs = m_se[[1]]; + P_eggs.std_error = m_se[[2]]; + F1_eggs = m_se[[3]]; + F1_eggs.std_error = m_se[[4]]; + F2_eggs = m_se[[5]]; + F2_eggs.std_error = m_se[[6]]; + } + if (process_young_nymphs) { + m_se = get_mean_and_std_error(P_young_nymphs.replications, F1_young_nymphs.replications, F2_young_nymphs.replications); + P_young_nymphs = m_se[[1]]; + P_young_nymphs.std_error = m_se[[2]]; + F1_young_nymphs = m_se[[3]]; + F1_young_nymphs.std_error = m_se[[4]]; + F2_young_nymphs = m_se[[5]]; + F2_young_nymphs.std_error = m_se[[6]]; } - if (process_nymphs) { - # Mean value for P nymphs. - P_nymphs = apply(P_nymphs.replications, 1, mean); - # Standard error for P_nymphs. - P_nymphs.std_error = apply(P_nymphs.replications, 1, sd) / sqrt(opt$replications); - # Mean value for F1 nymphs. - F1_nymphs = apply(F1_nymphs.replications, 1, mean); - # Standard error for F1 nymphs. - F1_nymphs.std_error = apply(F1_nymphs.replications, 1, sd) / sqrt(opt$replications); - # Mean value for F2 nymphs. - F2_nymphs = apply(F2_nymphs.replications, 1, mean); - # Standard error for F2 eggs. - F2_nymphs.std_error = apply(F2_nymphs.replications, 1, sd) / sqrt(opt$replications); + if (process_old_nymphs) { + m_se = get_mean_and_std_error(P_old_nymphs.replications, F1_old_nymphs.replications, F2_old_nymphs.replications); + P_old_nymphs = m_se[[1]]; + P_old_nymphs.std_error = m_se[[2]]; + F1_old_nymphs = m_se[[3]]; + F1_old_nymphs.std_error = m_se[[4]]; + F2_old_nymphs = m_se[[5]]; + F2_old_nymphs.std_error = m_se[[6]]; + } + if (process_total_nymphs) { + m_se = get_mean_and_std_error(P_total_nymphs.replications, F1_total_nymphs.replications, F2_total_nymphs.replications); + P_total_nymphs = m_se[[1]]; + P_total_nymphs.std_error = m_se[[2]]; + F1_total_nymphs = m_se[[3]]; + F1_total_nymphs.std_error = m_se[[4]]; + F2_total_nymphs = m_se[[5]]; + F2_total_nymphs.std_error = m_se[[6]]; } if (process_adults) { - # Mean value for P 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$replications); # Mean value for F1 adults. F1_adults = apply(F1_adults.replications, 1, mean); - # Standard error for F1 adults. + # Standard error for F1_adults. F1_adults.std_error = apply(F1_adults.replications, 1, sd) / sqrt(opt$replications); - # Mean value for F2 adults. + # Mean value for F2_adults. F2_adults = apply(F2_adults.replications, 1, mean); - # Standard error for F2 adults. + # Standard error for F2_adults. F2_adults.std_error = apply(F2_adults.replications, 1, sd) / sqrt(opt$replications); } } @@ -946,8 +1076,11 @@ start_date = temperature_data_frame$DATE[1]; end_date = temperature_data_frame$DATE[opt$num_days]; +cat("life_stages: ", toString(life_stages), "\n"); +cat("plot_generations_separately: ", plot_generations_separately, "\n"); if (plot_generations_separately) { for (life_stage in life_stages) { + cat("life_stage: ", life_stage, "\n"); if (life_stage == "Egg") { # Start PDF device driver. dev.new(width=20, height=30); @@ -956,6 +1089,15 @@ 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; + cat("maxval: ", maxval, "\n"); + cat("P_eggs: ", toString(P_eggs), "\n"); + cat("is.vector(P_eggs): ", is.vector(P_eggs), "\n"); + cat("length(P_eggs): ", length(P_eggs), "\n"); + cat("P_eggs.std_error: ", toString(P_eggs.std_error), "\n"); + cat("F1_eggs: ", toString(F1_eggs), "\n"); + cat("F1_eggs.std_error: ", toString(F1_eggs.std_error), "\n"); + cat("F2_eggs: ", toString(F2_eggs), "\n"); + cat("F2_eggs.std_error: ", toString(F2_eggs.std_error), "\n"); 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_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); @@ -963,16 +1105,44 @@ dev.off(); } else if (life_stage == "Nymph") { for (life_stage_nymph in life_stages_nymph) { + cat("life_stage_nymph: ", life_stage_nymph, "\n"); # Start PDF device driver. dev.new(width=20, height=30); 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; + if (life_stage_nymph=="Young") { + # Young nymph population size by generation. + maxval = max(P_young_nymphs+F1_young_nymphs+F2_young_nymphs) + 100; + group = P_young_nymphs; + group_std_error = P_young_nymphs.std_error; + group2 = F1_young_nymphs; + group2_std_error = F1_young_nymphs.std_error; + group3 = F2_young_nymphs; + group3_std_error = F2_young_nymphs.std_error; + } else if (life_stage_nymph=="Old") { + # Total nymph population size by generation. + maxval = max(P_old_nymphs+F1_old_nymphs+F2_old_nymphs) + 100; + group = P_old_nymphs; + group_std_error = P_old_nymphs.std_error; + group2 = F1_old_nymphs; + group2_std_error = F1_old_nymphs.std_error; + group3 = F2_old_nymphs; + group3_std_error = F2_old_nymphs.std_error; + } else if (life_stage_nymph=="Total") { + # Total nymph population size by generation. + maxval = max(P_total_nymphs+F1_total_nymphs+F2_total_nymphs) + 100; + group = P_total_nymphs; + group_std_error = P_total_nymphs.std_error; + group2 = F1_total_nymphs; + group2_std_error = F1_total_nymphs.std_error; + group3 = F2_total_nymphs; + group3_std_error = F2_total_nymphs.std_error; + } + cat("XXX group: ", group, "\n"); 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=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. dev.off(); }