| Previous changeset 58:2194155309f4 (2018-11-09) Next changeset 60:393085589438 (2018-12-20) |
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insect_phenology_model.R insect_phenology_model.xml utils.R |
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| diff -r 2194155309f4 -r 892cf703be62 insect_phenology_model.R --- 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 |
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| b'@@ -250,63 +250,51 @@\n return(mortality.probability)\n }\n \n-#mortality.egg = function(temperature, adj=0) {\n-# # If no input from adjustment, default\n-# # value is 0 (data from Nielsen, 2008).\n-# T.mortality = c(15, 17, 20, 25, 27, 30, 33, 35);\n-# egg.mortality = c(50, 2, 1, 0, 0, 0, 5, 100);\n-# # Calculates slopes and intercepts for lines.\n-# slopes = NULL;\n-# intercepts = NULL;\n-# for (i in 1:length(T.mortality)) {\n-# slopes[i] = (egg.mortality[i+1] - egg.mortality[i]) / (T.mortality[i+1] - T.mortality[i]);\n-# intercepts[i] = -slopes[i] * T.mortality[i] + egg.mortality[i];\n-# }\n-# # Calculates mortality based on temperature.\n-# mortality.probability = NULL;\n-# for (j in 1:length(temperature)) {\n-# mortality.probability[j] = if(temperature[j] <= T.mortality[2]) {\n-# temperature[j] * slopes[1] + intercepts[1];\n-# } else if (temperature[j] > T.mortality[2] && temperature[j] <= T.mortality[3]) {\n-# temperature[j] * slopes[2] + intercepts[2];\n-# } else if (temperature[j] > T.mortality[3] && temperature[j] <= T.mortality[4]) {\n-# temperature[j] * slopes[3] + intercepts[3];\n-# } else if (temperature[j] > T.mortality[4] && temperature[j] <= T.mortality[5]) {\n-# temperature[j] * slopes[4] + intercepts[4];\n-# } else if (temperature[j] > T.mortality[5] && temperature[j] <= T.mortality[6]) {\n-# temperature[j] * slopes[5] + intercepts[5];\n-# } else if (temperature[j] > T.mortality[6] && temperature[j] <= T.mortality[7]) {\n-# temperature[j] * slopes[6] + intercepts[6];\n-# } else if (temperature[j] > T.mortality[7]) {\n-# temperature[j] * slopes[7] + intercepts[7];\n-# }\n-# # If mortality > 100, make it equal to 100.\n-# mortality.probability[mortality.probability>100] = 100;\n-# # If mortality <0, make equal to 0.\n-# mortality.probability[mortality.probability<0] = 0;\n-# }\n-# # Make mortality adjustments based on adj parameter.\n-# mortality.probability = (100 - mortality.probability) * adj + mortality.probability;\n-# # if mortality > 100, make it equal to 100.\n-# mortality.probability[mortality.probability>100] = 100;\n-# # If mortality <0, make equal to 0.\n-# mortality.probability[mortality.probability<0] = 0;\n-# # Change percent to proportion.\n-# mortality.probability = mortality.probability / 100;\n-# return(mortality.probability)\n-#}\n-\n-mortality.egg = function(temperature) {\n- if (temperature < 12.7) {\n- mortality.probability = 0.8;\n+mortality.egg = function(temperature, adj=0) {\n+ # If no input from adjustment, default\n+ # value is 0 (data from Nielsen, 2008).\n+ T.mortality = c(15, 17, 20, 25, 27, 30, 33, 35);\n+ egg.mortality = c(50, 2, 1, 0, 0, 0, 5, 100);\n+ # Calculates slopes and intercepts for lines.\n+ slopes = NULL;\n+ intercepts = NULL;\n+ for (i in 1:length(T.mortality)) {\n+ slopes[i] = (egg.mortality[i+1] - egg.mortality[i]) / (T.mortality[i+1] - T.mortality[i]);\n+ intercepts[i] = -slopes[i] * T.mortality[i] + egg.mortality[i];\n }\n- else {\n- mortality.probability = 0.8 - temperature / 40.0;\n- if (mortality.probability < 0) {\n- mortality.probability = 0.01;\n- }\n+ # Calculates mortality based on temperature.\n+ mortality.probability = NULL;\n+ for (j in 1:length(temperature)) {\n+ mortality.probability[j] = if(temperature[j] <= T.mortality[2]) {\n+ temperature[j] * slopes[1] + intercepts[1];\n+ } else if (temperature[j] > T.mortality[2] && temperature[j] <= T.mortality[3]) {\n+ temperature[j] * slopes[2] + intercepts[2];'..b' if (vector.individual[3] >= (200+opt$adult_accumulation)) {\n+ # From old to adult, degree_days requirement met.\n+ current.gen = vector.individual[1];\n+ if (vector.individual[5] == 0) {\n+ # Previttelogenic.\n+ vector.individual = c(current.gen, 3, 0, 0, 0);\n+ }\n+ else {\n+ # Diapausing.\n+ vector.individual = c(current.gen, 5, 0, 0, 1);\n+ }\n+ }\n+ else {\n+ # Add 1 day in current stage.\n+ vector.individual[4] = vector.individual[4] + 1;\n+ }\n+ vector.matrix[i,] = vector.individual;\n }\n- vector.matrix[i,] = vector.individual;\n- }\n- # Growing of diapausing adult (unimportant, but still necessary).\n- if (vector.individual[2] == 5) {\n- vector.individual[3] = vector.individual[3] + averages.temp;\n- vector.individual[4] = vector.individual[4] + 1;\n- vector.matrix[i,] = vector.individual;\n- }\n- } # Else if it is still alive.\n- } # End of the individual bug loop.\n+ # Growing of diapausing adult (unimportant, but still necessary).\n+ if (vector.individual[2] == 5) {\n+ vector.individual[3] = vector.individual[3] + averages.temp;\n+ vector.individual[4] = vector.individual[4] + 1;\n+ vector.matrix[i,] = vector.individual;\n+ }\n+ } # Else if it is still alive.\n+ } # End of the individual bug loop.\n \n- # Number of deaths.\n- num_insects.death = length(death.vector);\n- if (num_insects.death > 0) {\n- # Remove record of dead.\n- vector.matrix = vector.matrix[-death.vector,];\n+ # Number of deaths.\n+ num_insects.death = length(death.vector);\n+ if (num_insects.death > 0) {\n+ # Remove record of dead.\n+ vector.matrix = vector.matrix[-death.vector,];\n+ }\n+ # Number of births.\n+ num_insects.newborn = length(birth.vector[,1]);\n+ vector.matrix = rbind(vector.matrix, birth.vector);\n+ # Update population size for the next day.\n+ num_insects = num_insects - num_insects.death + num_insects.newborn;\n+ } else {\n+ if (is.null(doy_zero_insects)) {\n+ # Only set the doy for zero insects if\n+ # it has not yet been set.\n+ doy_zero_insects = doy;\n+ }\n }\n- # Number of births.\n- num_insects.newborn = length(birth.vector[,1]);\n- vector.matrix = rbind(vector.matrix, birth.vector);\n- # Update population size for the next day.\n- num_insects = num_insects - num_insects.death + num_insects.newborn;\n \n # Aggregate results by day. Due to multiple transpose calls\n # on vector.matrix above, the columns of vector.matrix\n@@ -1547,7 +1539,12 @@\n write.csv(temperature_data_frame_F2, file=file_path, row.names=F);\n }\n \n+# Get the ticks date labels for plots.\n+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);\n+ticks = c(unlist(ticks_and_labels[1]));\n+date_labels = c(unlist(ticks_and_labels[2]));\n total_days_vector = c(1:dim(temperature_data_frame)[1]);\n+\n if (plot_generations_separately) {\n for (life_stage in life_stages) {\n if (life_stage == "Egg") {\n' |
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| diff -r 2194155309f4 -r 892cf703be62 insect_phenology_model.xml --- 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 |
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| @@ -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"/> |
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| diff -r 2194155309f4 -r 892cf703be62 utils.R --- a/utils.R Fri Nov 09 13:05:31 2018 -0500 +++ b/utils.R Wed Nov 21 11:42:37 2018 -0500 |
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| @@ -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. |