insect_phenology_model: insect_phenology

comparison insect_phenology_model.R @ 142:b06b3881ecf0 draft

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author	greg
date	Thu, 20 Dec 2018 09:08:50 -0500
parents	14afb6e85581
children	7628ba67c7ff

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-:14afb6e85581
+:b06b3881ecf0
 mortality.probability = temperature * 0.0005 + 0.02;
 }
 return(mortality.probability)
 }
-mortality.egg = function(temperature, adj=0) {
+#mortality.egg = function(temperature, adj=0) {
-# If no input from adjustment, default
+#    # If no input from adjustment, default
-# value is 0 (data from Nielsen, 2008).
+#    # value is 0 (data from Nielsen, 2008).
-T.mortality = c(15, 17, 20, 25, 27, 30, 33, 35);
+#    T.mortality = c(15, 17, 20, 25, 27, 30, 33, 35);
-egg.mortality = c(50, 2, 1, 0, 0, 0, 5, 100);
+#    egg.mortality = c(50, 2, 1, 0, 0, 0, 5, 100);
-# Calculates slopes and intercepts for lines.
+#    # Calculates slopes and intercepts for lines.
-slopes = NULL;
+#    slopes = NULL;
-intercepts = NULL;
+#    intercepts = NULL;
-for (i in 1:length(T.mortality)) {
+#    for (i in 1:length(T.mortality)) {
-slopes[i] = (egg.mortality[i+1] - egg.mortality[i]) / (T.mortality[i+1] - T.mortality[i]);
+#        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];
+#        intercepts[i] = -slopes[i] * T.mortality[i] + egg.mortality[i];
-}
+#    }
-# Calculates mortality based on temperature.
+#    # Calculates mortality based on temperature.
-mortality.probability = NULL;
+#    mortality.probability = NULL;
-for (j in 1:length(temperature)) {
+#    for (j in 1:length(temperature)) {
-mortality.probability[j] = if(temperature[j] <= T.mortality[2]) {
+#        mortality.probability[j] = if(temperature[j] <= T.mortality[2]) {
-temperature[j] * slopes[1] + intercepts[1];
+#                           temperature[j] * slopes[1] + intercepts[1];
-} else if (temperature[j] > T.mortality[2] && temperature[j] <= T.mortality[3]) {
+#                       } else if (temperature[j] > T.mortality[2] && temperature[j] <= T.mortality[3]) {
-temperature[j] * slopes[2] + intercepts[2];
+#                           temperature[j] * slopes[2] + intercepts[2];
-} else if (temperature[j] > T.mortality[3] && temperature[j] <= T.mortality[4]) {
+#                       } else if (temperature[j] > T.mortality[3] && temperature[j] <= T.mortality[4]) {
-temperature[j] * slopes[3] + intercepts[3];
+#                           temperature[j] * slopes[3] + intercepts[3];
-} else if (temperature[j] > T.mortality[4] && temperature[j] <= T.mortality[5]) {
+#                       } else if (temperature[j] > T.mortality[4] && temperature[j] <= T.mortality[5]) {
-temperature[j] * slopes[4] + intercepts[4];
+#                           temperature[j] * slopes[4] + intercepts[4];
-} else if (temperature[j] > T.mortality[5] && temperature[j] <= T.mortality[6]) {
+#                       } else if (temperature[j] > T.mortality[5] && temperature[j] <= T.mortality[6]) {
-temperature[j] * slopes[5] + intercepts[5];
+#                           temperature[j] * slopes[5] + intercepts[5];
-} else if (temperature[j] > T.mortality[6] && temperature[j] <= T.mortality[7]) {
+#                       } else if (temperature[j] > T.mortality[6] && temperature[j] <= T.mortality[7]) {
-temperature[j] * slopes[6] + intercepts[6];
+#                           temperature[j] * slopes[6] + intercepts[6];
-} else if (temperature[j] > T.mortality[7]) {
+#                       } else if (temperature[j] > T.mortality[7]) {
-temperature[j] * slopes[7] + intercepts[7];
+#                           temperature[j] * slopes[7] + intercepts[7];
-}
+#                       }
-# If mortality > 100, make it equal to 100.
+#        # If mortality > 100, make it equal to 100.
-mortality.probability[mortality.probability>100] = 100;
+#        mortality.probability[mortality.probability>100] = 100;
-# If mortality <0, make equal to 0.
+#        # If mortality <0, make equal to 0.
-mortality.probability[mortality.probability<0] = 0;
+#        mortality.probability[mortality.probability<0] = 0;
-}
+#    }
-# Make mortality adjustments based on adj parameter.
+#    # Make mortality adjustments based on adj parameter.
-mortality.probability = (100 - mortality.probability) * adj + mortality.probability;
+#    mortality.probability = (100 - mortality.probability) * adj + mortality.probability;
-# if mortality > 100, make it equal to 100.
+#    # if mortality > 100, make it equal to 100.
-mortality.probability[mortality.probability>100] = 100;
+#    mortality.probability[mortality.probability>100] = 100;
-# If mortality <0, make equal to 0.
+#    # If mortality <0, make equal to 0.
-mortality.probability[mortality.probability<0] = 0;
+#    mortality.probability[mortality.probability<0] = 0;
-# Change percent to proportion.
+#    # Change percent to proportion.
-mortality.probability = mortality.probability / 100;
+#    mortality.probability = mortality.probability / 100;
-return(mortality.probability)
+#    return(mortality.probability)
+#}
+mortality.egg = function(temperature) {
+if (temperature < 12.7) {
+mortality.probability = 0.8;
+} else {
+mortality.probability = 0.8 - temperature / 40.0;
+if (mortality.probability < 0) {
+mortality.probability = 0.01;
+}
+}
+return (mortality.probability);
 }
 mortality.nymph = function(temperature) {
 if (temperature < 12.7) {
 mortality.probability = 0.03;
 parse_input_data = function(input_ytd, input_norm, location, start_date, end_date) {
 # The end DOY for norm data prepended to ytd data.
 prepend_end_doy_norm = 0;
 # The start DOY for norm data appended to ytd data.
 append_start_doy_norm = 0;
+cat("start_date: ", start_date, "\n");
+cat("end_date: ", end_date, "\n");
 if (is.null(start_date) && is.null(end_date)) {
 # We're not dealing with a date interval.
 date_interval = FALSE;
 if (is.null(input_ytd)) {
 # Base all dates on the current date since 30 year
 year = get_year_from_date(start_date);
 # Get the DOY for start_date and end_date.
 start_date_doy = as.integer(strftime(start_date, format="%j"));
 end_date_doy = as.integer(strftime(end_date, format="%j"));
 }
+cat("date_interval: ", date_interval, "\n");
 if (is.null(input_ytd)) {
 # We're processing only the 30 year normals data.
 processing_year_to_date_data = FALSE;
 if (is.null(start_date) && is.null(end_date)) {
 # We're processing the entire year, so we can
 start_date_ytd_row = 0;
 start_date_norm_row = which(norm_data_frame$DOY==start_date_doy);
 }
 end_date_ytd_row = which(temperature_data_frame$DATE==end_date);
 if (length(end_date_ytd_row) > 0) {
+cat("I'm here...\n");
 end_date_ytd_row = end_date_ytd_row[1];
 # The end date is contained within the input_ytd data.
 end_doy_ytd = as.integer(temperature_data_frame$DOY[end_date_ytd_row]);
-if (end_doy_ytd > end_date_ytd_row + 1) {
+cat("end_doy_ytd: ", end_doy_ytd, "\n");
-# The input year-to-date dataset is missing 1 or more
+cat("end_date_ytd_row: ", end_date_ytd_row, "\n");
-# days of data.
+cat("start_date_ytd_row: ", start_date_ytd_row, "\n");
-days_missing = end_doy_ytd - end_date_ytd_row;
-msg = cat("The year-to-date dataset is missing ", days_missing, " days of data.\n");
-stop_err(msg);
-}
 } else {
 end_date_ytd_row = 0;
 }
 } else {
 # We're plotting an entire year.
 # Properly set the end_date to be Dec 31 of the year.
 end_date = paste(year, "12", "31", sep="-");
 # Save the first DOY to later check if start_date is Jan 1.
 start_doy_ytd = as.integer(temperature_data_frame$DOY[1]);
 end_doy_ytd = as.integer(temperature_data_frame$DOY[num_ytd_rows]);
-if (end_doy_ytd > end_date_ytd_row + 1) {
+cat("I'm here 2...\n");
-# The input year-to-date dataset is missing 1 or more
+cat("end_doy_ytd: ", end_doy_ytd, "\n");
-# days of data.
+cat("end_date_ytd_row: ", end_date_ytd_row, "\n");
-days_missing = end_doy_ytd - end_date_ytd_row;
+cat("start_date_ytd_row: ", start_date_ytd_row, "\n");
-msg = cat("The year-to-date dataset is missing ", days_missing, " days of data.\n");
-stop_err(msg);
-}
 }
 } else {
 # We're processing only the 30 year normals data, so create an empty
 # data frame for containing temperature data after it is converted
 # from the 30 year normals format to the year-to-date format.
 for (i in 1:total_days) {
 temperature_data_frame[i,] = get_next_normals_row(norm_data_frame, year, i);
 }
 }
 }
+# Ensure all DOY values are consectuive integers.
+validate_doys(temperature_data_frame);
 # Add a column containing the daylight length for each day.
 temperature_data_frame = add_daylight_length(temperature_data_frame);
 return(list(temperature_data_frame, start_date, end_date, prepend_end_doy_norm, append_start_doy_norm, is_leap_year, location));
 }
 post.mortality = 2;
 day.kill = 250;
 }
 if (vector.individual[2] == 0) {
 # Egg.
-death.probability = opt$egg_mortality * mortality.egg(mean.temp, adj=opt$egg_mortality);
+# death.probability = opt$egg_mortality * mortality.egg(mean.temp, 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);
 }

Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 142:b06b3881ecf0 draft