Mercurial > repos > greg > insect_phenology_model
changeset 59:892cf703be62 draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 21 Nov 2018 11:42:37 -0500 |
| parents | 2194155309f4 |
| children | 393085589438 |
| files | insect_phenology_model.R insect_phenology_model.xml utils.R |
| diffstat | 3 files changed, 271 insertions(+), 256 deletions(-) [+] |
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--- a/insect_phenology_model.R Fri Nov 09 13:05:31 2018 -0500 +++ b/insect_phenology_model.R Wed Nov 21 11:42:37 2018 -0500 @@ -250,63 +250,51 @@ return(mortality.probability) } -#mortality.egg = function(temperature, adj=0) { -# # If no input from adjustment, default -# # value is 0 (data from Nielsen, 2008). -# T.mortality = c(15, 17, 20, 25, 27, 30, 33, 35); -# egg.mortality = c(50, 2, 1, 0, 0, 0, 5, 100); -# # Calculates slopes and intercepts for lines. -# slopes = NULL; -# intercepts = NULL; -# for (i in 1:length(T.mortality)) { -# slopes[i] = (egg.mortality[i+1] - egg.mortality[i]) / (T.mortality[i+1] - T.mortality[i]); -# intercepts[i] = -slopes[i] * T.mortality[i] + egg.mortality[i]; -# } -# # Calculates mortality based on temperature. -# mortality.probability = NULL; -# for (j in 1:length(temperature)) { -# mortality.probability[j] = if(temperature[j] <= T.mortality[2]) { -# temperature[j] * slopes[1] + intercepts[1]; -# } else if (temperature[j] > T.mortality[2] && temperature[j] <= T.mortality[3]) { -# temperature[j] * slopes[2] + intercepts[2]; -# } else if (temperature[j] > T.mortality[3] && temperature[j] <= T.mortality[4]) { -# temperature[j] * slopes[3] + intercepts[3]; -# } else if (temperature[j] > T.mortality[4] && temperature[j] <= T.mortality[5]) { -# temperature[j] * slopes[4] + intercepts[4]; -# } else if (temperature[j] > T.mortality[5] && temperature[j] <= T.mortality[6]) { -# temperature[j] * slopes[5] + intercepts[5]; -# } else if (temperature[j] > T.mortality[6] && temperature[j] <= T.mortality[7]) { -# temperature[j] * slopes[6] + intercepts[6]; -# } else if (temperature[j] > T.mortality[7]) { -# temperature[j] * slopes[7] + intercepts[7]; -# } -# # If mortality > 100, make it equal to 100. -# mortality.probability[mortality.probability>100] = 100; -# # If mortality <0, make equal to 0. -# mortality.probability[mortality.probability<0] = 0; -# } -# # Make mortality adjustments based on adj parameter. -# mortality.probability = (100 - mortality.probability) * adj + mortality.probability; -# # if mortality > 100, make it equal to 100. -# mortality.probability[mortality.probability>100] = 100; -# # If mortality <0, make equal to 0. -# mortality.probability[mortality.probability<0] = 0; -# # Change percent to proportion. -# mortality.probability = mortality.probability / 100; -# return(mortality.probability) -#} - -mortality.egg = function(temperature) { - if (temperature < 12.7) { - mortality.probability = 0.8; +mortality.egg = function(temperature, adj=0) { + # If no input from adjustment, default + # value is 0 (data from Nielsen, 2008). + T.mortality = c(15, 17, 20, 25, 27, 30, 33, 35); + egg.mortality = c(50, 2, 1, 0, 0, 0, 5, 100); + # Calculates slopes and intercepts for lines. + slopes = NULL; + intercepts = NULL; + for (i in 1:length(T.mortality)) { + slopes[i] = (egg.mortality[i+1] - egg.mortality[i]) / (T.mortality[i+1] - T.mortality[i]); + intercepts[i] = -slopes[i] * T.mortality[i] + egg.mortality[i]; } - else { - mortality.probability = 0.8 - temperature / 40.0; - if (mortality.probability < 0) { - mortality.probability = 0.01; - } + # Calculates mortality based on temperature. + mortality.probability = NULL; + for (j in 1:length(temperature)) { + mortality.probability[j] = if(temperature[j] <= T.mortality[2]) { + temperature[j] * slopes[1] + intercepts[1]; + } else if (temperature[j] > T.mortality[2] && temperature[j] <= T.mortality[3]) { + temperature[j] * slopes[2] + intercepts[2]; + } else if (temperature[j] > T.mortality[3] && temperature[j] <= T.mortality[4]) { + temperature[j] * slopes[3] + intercepts[3]; + } else if (temperature[j] > T.mortality[4] && temperature[j] <= T.mortality[5]) { + temperature[j] * slopes[4] + intercepts[4]; + } else if (temperature[j] > T.mortality[5] && temperature[j] <= T.mortality[6]) { + temperature[j] * slopes[5] + intercepts[5]; + } else if (temperature[j] > T.mortality[6] && temperature[j] <= T.mortality[7]) { + temperature[j] * slopes[6] + intercepts[6]; + } else if (temperature[j] > T.mortality[7]) { + temperature[j] * slopes[7] + intercepts[7]; + } + # If mortality > 100, make it equal to 100. + mortality.probability[mortality.probability>100] = 100; + # If mortality <0, make equal to 0. + mortality.probability[mortality.probability<0] = 0; } + # Make mortality adjustments based on adj parameter. + mortality.probability = (100 - mortality.probability) * adj + mortality.probability; + # if mortality > 100, make it equal to 100. + mortality.probability[mortality.probability>100] = 100; + # If mortality <0, make equal to 0. + mortality.probability[mortality.probability<0] = 0; + # Change percent to proportion. + mortality.probability = mortality.probability / 100; return(mortality.probability) +} mortality.nymph = function(temperature) { if (temperature < 12.7) { @@ -614,10 +602,6 @@ cat("Number of days in year: ", num_days, "\n"); } -# Get the ticks date labels for plots. -ticks_and_labels = get_x_axis_ticks_and_labels(temperature_data_frame, prepend_end_doy_norm, append_start_doy_norm); -ticks = c(unlist(ticks_and_labels[1])); -date_labels = c(unlist(ticks_and_labels[2])); # All latitude values are the same, so get the value for plots from the first row. latitude = temperature_data_frame$LATITUDE[1]; @@ -756,6 +740,7 @@ # Total population. population.replications = matrix(rep(0, total_days*opt$replications), ncol=opt$replications); +doy_zero_insects = NULL; # Process replications. for (current_replication in 1:opt$replications) { # Start with the user-defined number of insects per replication. @@ -856,218 +841,225 @@ # Newborn. birth.vector = NULL; # All individuals. - for (i in 1:num_insects) { - # Individual record. - vector.individual = vector.matrix[i,]; - # Adjustment for late season mortality rate (still alive?). - if (latitude < 40.0) { - post.mortality = 1; - day.kill = 300; - } - else { - post.mortality = 2; - day.kill = 250; - } - if (vector.individual[2] == 0) { - # Egg. - #death.probability = opt$egg_mortality * mortality.egg(mean.temp, adj=opt$egg_mortality); - death.probability = opt$egg_mortality * mortality.egg(mean.temp); - } - else if (vector.individual[2] == 1 | vector.individual[2] == 2) { - # Nymph. - death.probability = opt$nymph_mortality * mortality.nymph(mean.temp); - } - else if (vector.individual[2] == 3 | vector.individual[2] == 4 | vector.individual[2] == 5) { - # Adult. - if (doy < day.kill) { - death.probability = opt$adult_mortality * mortality.adult(mean.temp); + if (num_insects > 0) { + for (i in 1:num_insects) { + # Individual record. + vector.individual = vector.matrix[i,]; + # Adjustment for late season mortality rate (still alive?). + if (latitude < 40.0) { + post.mortality = 1; + day.kill = 300; + } + else { + post.mortality = 2; + day.kill = 250; + } + if (vector.individual[2] == 0) { + # Egg. + death.probability = opt$egg_mortality * mortality.egg(mean.temp, adj=opt$egg_mortality); + } + else if (vector.individual[2] == 1 | vector.individual[2] == 2) { + # Nymph. + death.probability = opt$nymph_mortality * mortality.nymph(mean.temp); + } + else if (vector.individual[2] == 3 | vector.individual[2] == 4 | vector.individual[2] == 5) { + # Adult. + if (doy < day.kill) { + death.probability = opt$adult_mortality * mortality.adult(mean.temp); + } + else { + # Increase adult mortality after fall equinox. + death.probability = opt$adult_mortality * post.mortality * mortality.adult(mean.temp); + } + } + # Dependent on temperature and life stage? + u.d = runif(1); + if (u.d < death.probability) { + death.vector = c(death.vector, i); } else { - # Increase adult mortality after fall equinox. - death.probability = opt$adult_mortality * post.mortality * mortality.adult(mean.temp); - } - } - # Dependent on temperature and life stage? - u.d = runif(1); - if (u.d < death.probability) { - death.vector = c(death.vector, i); - } - else { - # End of diapause. - if (vector.individual[1] == 0 && vector.individual[2] == 3) { - # Overwintering adult (pre-vittelogenic). - if (photoperiod > opt$photoperiod && vector.individual[3] > 68 && doy < 180) { - # Add 68C to become fully reproductively matured. - # Transfer to vittelogenic. - vector.individual = c(0, 4, 0, 0, 0); - vector.matrix[i,] = vector.individual; + # End of diapause. + if (vector.individual[1] == 0 && vector.individual[2] == 3) { + # Overwintering adult (pre-vittelogenic). + if (photoperiod > opt$photoperiod && vector.individual[3] > 68 && doy < 180) { + # Add 68C to become fully reproductively matured. + # Transfer to vittelogenic. + vector.individual = c(0, 4, 0, 0, 0); + vector.matrix[i,] = vector.individual; + } + else { + # Add average temperature for current day. + vector.individual[3] = vector.individual[3] + averages.temp; + # Add 1 day in current stage. + vector.individual[4] = vector.individual[4] + 1; + vector.matrix[i,] = vector.individual; + } } - else { - # Add average temperature for current day. - vector.individual[3] = vector.individual[3] + averages.temp; - # Add 1 day in current stage. - vector.individual[4] = vector.individual[4] + 1; - vector.matrix[i,] = vector.individual; + if (vector.individual[1] != 0 && vector.individual[2] == 3) { + # Not overwintering adult (pre-vittelogenic). + current.gen = vector.individual[1]; + if (vector.individual[3] > 68) { + # Add 68C to become fully reproductively matured. + # Transfer to vittelogenic. + vector.individual = c(current.gen, 4, 0, 0, 0); + vector.matrix[i,] = vector.individual; + } + else { + # Add average temperature for current day. + vector.individual[3] = vector.individual[3] + averages.temp; + # Add 1 day in current stage. + vector.individual[4] = vector.individual[4] + 1; + vector.matrix[i,] = vector.individual; + } } - } - if (vector.individual[1] != 0 && vector.individual[2] == 3) { - # Not overwintering adult (pre-vittelogenic). - current.gen = vector.individual[1]; - if (vector.individual[3] > 68) { - # Add 68C to become fully reproductively matured. - # Transfer to vittelogenic. - vector.individual = c(current.gen, 4, 0, 0, 0); - vector.matrix[i,] = vector.individual; - } - else { + # Oviposition -- where population dynamics comes from. + if (vector.individual[2] == 4 && vector.individual[1] == 0 && mean.temp > 10) { + # Vittelogenic stage, overwintering generation. + if (vector.individual[4] == 0) { + # Just turned in vittelogenic stage. + num_insects.birth = round(runif(1, 2 + opt$min_clutch_size, 8 + opt$max_clutch_size)); + } + else { + # Daily probability of birth. + p.birth = opt$oviposition * 0.01; + u1 = runif(1); + if (u1 < p.birth) { + num_insects.birth = round(runif(1, 2, 8)); + } + } # Add average temperature for current day. vector.individual[3] = vector.individual[3] + averages.temp; # Add 1 day in current stage. vector.individual[4] = vector.individual[4] + 1; vector.matrix[i,] = vector.individual; - } - } - # Oviposition -- where population dynamics comes from. - if (vector.individual[2] == 4 && vector.individual[1] == 0 && mean.temp > 10) { - # Vittelogenic stage, overwintering generation. - if (vector.individual[4] == 0) { - # Just turned in vittelogenic stage. - num_insects.birth = round(runif(1, 2 + opt$min_clutch_size, 8 + opt$max_clutch_size)); - } - else { - # Daily probability of birth. - p.birth = opt$oviposition * 0.01; - u1 = runif(1); - if (u1 < p.birth) { - num_insects.birth = round(runif(1, 2, 8)); + if (num_insects.birth > 0) { + # Add new birth -- might be in different generations. + new.gen = vector.individual[1] + 1; + # Egg profile. + new.individual = c(new.gen, 0, 0, 0, 0); + new.vector = rep(new.individual, num_insects.birth); + # Update batch of egg profile. + new.vector = t(matrix(new.vector, nrow=5)); + # Group with total eggs laid in that day. + birth.vector = rbind(birth.vector, new.vector); } } - # Add average temperature for current day. - vector.individual[3] = vector.individual[3] + averages.temp; - # Add 1 day in current stage. - vector.individual[4] = vector.individual[4] + 1; - vector.matrix[i,] = vector.individual; - if (num_insects.birth > 0) { - # Add new birth -- might be in different generations. - new.gen = vector.individual[1] + 1; - # Egg profile. - new.individual = c(new.gen, 0, 0, 0, 0); - new.vector = rep(new.individual, num_insects.birth); - # Update batch of egg profile. - new.vector = t(matrix(new.vector, nrow=5)); - # Group with total eggs laid in that day. - birth.vector = rbind(birth.vector, new.vector); - } - } - # Oviposition -- for generation 1. - if (vector.individual[2] == 4 && vector.individual[1] == 1 && mean.temp > 12.5 && doy < 222) { - # Vittelogenic stage, 1st generation - if (vector.individual[4] == 0) { - # Just turned in vittelogenic stage. - num_insects.birth = round(runif(1, 2+opt$min_clutch_size, 8+opt$max_clutch_size)); - } - else { - # Daily probability of birth. - p.birth = opt$oviposition * 0.01; - u1 = runif(1); - if (u1 < p.birth) { - num_insects.birth = round(runif(1, 2, 8)); + # Oviposition -- for generation 1. + if (vector.individual[2] == 4 && vector.individual[1] == 1 && mean.temp > 12.5 && doy < 222) { + # Vittelogenic stage, 1st generation + if (vector.individual[4] == 0) { + # Just turned in vittelogenic stage. + num_insects.birth = round(runif(1, 2+opt$min_clutch_size, 8+opt$max_clutch_size)); + } + else { + # Daily probability of birth. + p.birth = opt$oviposition * 0.01; + u1 = runif(1); + if (u1 < p.birth) { + num_insects.birth = round(runif(1, 2, 8)); + } + } + # Add average temperature for current day. + vector.individual[3] = vector.individual[3] + averages.temp; + # Add 1 day in current stage. + vector.individual[4] = vector.individual[4] + 1; + vector.matrix[i,] = vector.individual; + if (num_insects.birth > 0) { + # Add new birth -- might be in different generations. + new.gen = vector.individual[1] + 1; + # Egg profile. + new.individual = c(new.gen, 0, 0, 0, 0); + new.vector = rep(new.individual, num_insects.birth); + # Update batch of egg profile. + new.vector = t(matrix(new.vector, nrow=5)); + # Group with total eggs laid in that day. + birth.vector = rbind(birth.vector, new.vector); } } - # Add average temperature for current day. - vector.individual[3] = vector.individual[3] + averages.temp; - # Add 1 day in current stage. - vector.individual[4] = vector.individual[4] + 1; - vector.matrix[i,] = vector.individual; - if (num_insects.birth > 0) { - # Add new birth -- might be in different generations. - new.gen = vector.individual[1] + 1; - # Egg profile. - new.individual = c(new.gen, 0, 0, 0, 0); - new.vector = rep(new.individual, num_insects.birth); - # Update batch of egg profile. - new.vector = t(matrix(new.vector, nrow=5)); - # Group with total eggs laid in that day. - birth.vector = rbind(birth.vector, new.vector); - } - } - # Egg to young nymph. - if (vector.individual[2] == 0) { - # Add average temperature for current day. - vector.individual[3] = vector.individual[3] + averages.temp; - if (vector.individual[3] >= (68+opt$young_nymph_accumulation)) { - # From egg to young nymph, degree-days requirement met. - current.gen = vector.individual[1]; - # Transfer to young nymph stage. - vector.individual = c(current.gen, 1, 0, 0, 0); - } - else { - # Add 1 day in current stage. - vector.individual[4] = vector.individual[4] + 1; + # Egg to young nymph. + if (vector.individual[2] == 0) { + # Add average temperature for current day. + vector.individual[3] = vector.individual[3] + averages.temp; + if (vector.individual[3] >= (68+opt$young_nymph_accumulation)) { + # From egg to young nymph, degree-days requirement met. + current.gen = vector.individual[1]; + # Transfer to young nymph stage. + vector.individual = c(current.gen, 1, 0, 0, 0); + } + else { + # Add 1 day in current stage. + vector.individual[4] = vector.individual[4] + 1; + } + vector.matrix[i,] = vector.individual; } - vector.matrix[i,] = vector.individual; - } - # Young nymph to old nymph. - if (vector.individual[2] == 1) { - # Add average temperature for current day. - vector.individual[3] = vector.individual[3] + averages.temp; - if (vector.individual[3] >= (250+opt$old_nymph_accumulation)) { - # From young to old nymph, degree_days requirement met. - current.gen = vector.individual[1]; - # Transfer to old nym stage. - vector.individual = c(current.gen, 2, 0, 0, 0); - if (photoperiod < opt$photoperiod && doy > 180) { - vector.individual[5] = 1; - } # Prepare for diapausing. - } - else { - # Add 1 day in current stage. - vector.individual[4] = vector.individual[4] + 1; - } - vector.matrix[i,] = vector.individual; - } - # Old nymph to adult: pre-vittelogenic or diapausing? - if (vector.individual[2] == 2) { - # Add average temperature for current day. - vector.individual[3] = vector.individual[3] + averages.temp; - if (vector.individual[3] >= (200+opt$adult_accumulation)) { - # From old to adult, degree_days requirement met. - current.gen = vector.individual[1]; - if (vector.individual[5] == 0) { - # Previttelogenic. - vector.individual = c(current.gen, 3, 0, 0, 0); + # Young nymph to old nymph. + if (vector.individual[2] == 1) { + # Add average temperature for current day. + vector.individual[3] = vector.individual[3] + averages.temp; + if (vector.individual[3] >= (250+opt$old_nymph_accumulation)) { + # From young to old nymph, degree_days requirement met. + current.gen = vector.individual[1]; + # Transfer to old nym stage. + vector.individual = c(current.gen, 2, 0, 0, 0); + if (photoperiod < opt$photoperiod && doy > 180) { + vector.individual[5] = 1; + } # Prepare for diapausing. } else { - # Diapausing. - vector.individual = c(current.gen, 5, 0, 0, 1); + # Add 1 day in current stage. + vector.individual[4] = vector.individual[4] + 1; } + vector.matrix[i,] = vector.individual; } - else { - # Add 1 day in current stage. - vector.individual[4] = vector.individual[4] + 1; + # Old nymph to adult: pre-vittelogenic or diapausing? + if (vector.individual[2] == 2) { + # Add average temperature for current day. + vector.individual[3] = vector.individual[3] + averages.temp; + if (vector.individual[3] >= (200+opt$adult_accumulation)) { + # From old to adult, degree_days requirement met. + current.gen = vector.individual[1]; + if (vector.individual[5] == 0) { + # Previttelogenic. + vector.individual = c(current.gen, 3, 0, 0, 0); + } + else { + # Diapausing. + vector.individual = c(current.gen, 5, 0, 0, 1); + } + } + else { + # Add 1 day in current stage. + vector.individual[4] = vector.individual[4] + 1; + } + vector.matrix[i,] = vector.individual; } - vector.matrix[i,] = vector.individual; - } - # Growing of diapausing adult (unimportant, but still necessary). - if (vector.individual[2] == 5) { - vector.individual[3] = vector.individual[3] + averages.temp; - vector.individual[4] = vector.individual[4] + 1; - vector.matrix[i,] = vector.individual; - } - } # Else if it is still alive. - } # End of the individual bug loop. + # Growing of diapausing adult (unimportant, but still necessary). + if (vector.individual[2] == 5) { + vector.individual[3] = vector.individual[3] + averages.temp; + vector.individual[4] = vector.individual[4] + 1; + vector.matrix[i,] = vector.individual; + } + } # Else if it is still alive. + } # End of the individual bug loop. - # Number of deaths. - num_insects.death = length(death.vector); - if (num_insects.death > 0) { - # Remove record of dead. - vector.matrix = vector.matrix[-death.vector,]; + # Number of deaths. + num_insects.death = length(death.vector); + if (num_insects.death > 0) { + # Remove record of dead. + vector.matrix = vector.matrix[-death.vector,]; + } + # Number of births. + num_insects.newborn = length(birth.vector[,1]); + vector.matrix = rbind(vector.matrix, birth.vector); + # Update population size for the next day. + num_insects = num_insects - num_insects.death + num_insects.newborn; + } else { + if (is.null(doy_zero_insects)) { + # Only set the doy for zero insects if + # it has not yet been set. + doy_zero_insects = doy; + } } - # Number of births. - num_insects.newborn = length(birth.vector[,1]); - vector.matrix = rbind(vector.matrix, birth.vector); - # Update population size for the next day. - num_insects = num_insects - num_insects.death + num_insects.newborn; # Aggregate results by day. Due to multiple transpose calls # on vector.matrix above, the columns of vector.matrix @@ -1547,7 +1539,12 @@ write.csv(temperature_data_frame_F2, file=file_path, row.names=F); } +# Get the ticks date labels for plots. +ticks_and_labels = get_x_axis_ticks_and_labels(temperature_data_frame, prepend_end_doy_norm=prepend_end_doy_norm, append_start_doy_norm=append_start_doy_norm, date_interval=FALSE, doy_zero_insects=doy_zero_insects); +ticks = c(unlist(ticks_and_labels[1])); +date_labels = c(unlist(ticks_and_labels[2])); total_days_vector = c(1:dim(temperature_data_frame)[1]); + if (plot_generations_separately) { for (life_stage in life_stages) { if (life_stage == "Egg") {
--- a/insect_phenology_model.xml Fri Nov 09 13:05:31 2018 -0500 +++ b/insect_phenology_model.xml Wed Nov 21 11:42:37 2018 -0500 @@ -82,7 +82,7 @@ <option value="BMSB" selected="True">Brown Marmorated Stink Bug</option> </param> <param name="replications" type="integer" value="10" min="2" label="Number of replications"/> - <param name="insects_per_replication" type="integer" value="1000" min="1" label="Number of insects with which to start each replication"/> + <param name="insects_per_replication" type="integer" value="1000" min="100" label="Number of insects with which to start each replication"/> <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination"/> <param name="egg_mortality" type="float" value="1" min="0" max="1" label="Adjustment rate for egg mortality" help="Floating point value between 0 and 1"/> <param name="nymph_mortality" type="float" value="1" min="0" label="Adjustment rate for nymph mortality"/>
--- a/utils.R Fri Nov 09 13:05:31 2018 -0500 +++ b/utils.R Wed Nov 21 11:42:37 2018 -0500 @@ -96,7 +96,7 @@ } } -get_x_axis_ticks_and_labels = function(temperature_data_frame, prepend_end_doy_norm=0, append_start_doy_norm=0, date_interval=FALSE) { +get_x_axis_ticks_and_labels = function(temperature_data_frame, prepend_end_doy_norm=0, append_start_doy_norm=0, date_interval=FALSE, doy_zero_insects=NULL) { # Generate a list of ticks and labels for plotting the x axis. if (prepend_end_doy_norm > 0) { prepend_end_norm_row = which(temperature_data_frame$DOY==prepend_end_doy_norm); @@ -108,6 +108,11 @@ } else { append_start_norm_row = 0; } + if (is.null(doy_zero_insects)) { + zero_insects_row = 0; + } else { + zero_insects_row = which(temperature_data_frame$DOY==doy_zero_insects); + } num_rows = dim(temperature_data_frame)[1]; tick_labels = list(); ticks = list(); @@ -130,11 +135,24 @@ doy = as.integer(temperature_data_frame$DOY[i]); # We're plotting the entire year, so ticks will # occur on Sundays and the first of each month. - if (i == prepend_end_norm_row) { + if (i == zero_insects_row) { + # Add a tick for the day on which the number of insects + # per replication is 0. + label_str = "Number insects is 0"; + tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep); + ticks[tick_index] = i; + if (date_interval) { + # Append the day to label_str + tick_labels[tick_index] = paste(label_str, day, sep=" "); + } else { + tick_labels[tick_index] = label_str; + } + last_tick = i; + } else if (i == prepend_end_norm_row) { # Add a tick for the end of the 30 year normnals data # that was prepended to the year-to-date data. label_str = "End prepended 30 year normals"; - tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep) + tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep); ticks[tick_index] = i; if (date_interval) { # Append the day to label_str @@ -147,7 +165,7 @@ # Add a tick for the start of the 30 year normnals data # that was appended to the year-to-date data. label_str = "Start appended 30 year normals"; - tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep) + tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep); ticks[tick_index] = i; if (!identical(current_month_label, month_label)) { # Append the month to label_str. @@ -163,7 +181,7 @@ } else if (i==num_rows) { # Add a tick for the last day of the year. label_str = ""; - tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep) + tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep); ticks[tick_index] = i; if (!identical(current_month_label, month_label)) { # Append the month to label_str. @@ -178,7 +196,7 @@ } else { if (!identical(current_month_label, month_label)) { # Add a tick for the month. - tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep) + tick_index = get_tick_index(i, last_tick, ticks, tick_labels, tick_sep); ticks[tick_index] = i; if (date_interval) { # Append the day to the month.