Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 63:c5df0777fa31 draft

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author greg
date Fri, 08 Nov 2019 13:01:48 -0500
parents 3116ddd4c26d
children 883d812611b3
comparison
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62:3116ddd4c26d 63:c5df0777fa31
249 } 249 }
250 return(mortality.probability) 250 return(mortality.probability)
251 } 251 }
252 252
253 mortality.egg = function(temperature, adj=0) { 253 mortality.egg = function(temperature, adj=0) {
254 if (adj == 0) { 254 # If no input from adjustment, default
255 # If no input from adjustment, default 255 # value is 0 (data from Nielsen, 2008).
256 # value is 0 (data from Nielsen, 2008). 256 T.mortality = c(15, 17, 20, 25, 27, 30, 33, 35);
257 T.mortality = c(15, 17, 20, 25, 27, 30, 33, 35); 257 egg.mortality = c(50, 2, 1, 0, 0, 0, 5, 100);
258 egg.mortality = c(50, 2, 1, 0, 0, 0, 5, 100); 258 # Calculates slopes and intercepts for lines.
259 # Calculates slopes and intercepts for lines. 259 slopes = NULL;
260 slopes = NULL; 260 intercepts = NULL;
261 intercepts = NULL; 261 for (i in 1:length(T.mortality)) {
262 for (i in 1:length(T.mortality)) { 262 slopes[i] = (egg.mortality[i+1] - egg.mortality[i]) / (T.mortality[i+1] - T.mortality[i]);
263 slopes[i] = (egg.mortality[i+1] - egg.mortality[i]) / (T.mortality[i+1] - T.mortality[i]); 263 intercepts[i] = -slopes[i] * T.mortality[i] + egg.mortality[i];
264 intercepts[i] = -slopes[i] * T.mortality[i] + egg.mortality[i]; 264 }
265 } 265 # Calculates mortality based on temperature.
266 # Calculates mortality based on temperature. 266 mortality.probability = NULL;
267 mortality.probability = NULL; 267 for (j in 1:length(temperature)) {
268 for (j in 1:length(temperature)) { 268 mortality.probability[j] = if(temperature[j] <= T.mortality[2]) {
269 mortality.probability[j] = if(temperature[j] <= T.mortality[2]) { 269 temperature[j] * slopes[1] + intercepts[1];
270 temperature[j] * slopes[1] + intercepts[1]; 270 } else if (temperature[j] > T.mortality[2] && temperature[j] <= T.mortality[3]) {
271 } else if (temperature[j] > T.mortality[2] && temperature[j] <= T.mortality[3]) { 271 temperature[j] * slopes[2] + intercepts[2];
272 temperature[j] * slopes[2] + intercepts[2]; 272 } else if (temperature[j] > T.mortality[3] && temperature[j] <= T.mortality[4]) {
273 } else if (temperature[j] > T.mortality[3] && temperature[j] <= T.mortality[4]) { 273 temperature[j] * slopes[3] + intercepts[3];
274 temperature[j] * slopes[3] + intercepts[3]; 274 } else if (temperature[j] > T.mortality[4] && temperature[j] <= T.mortality[5]) {
275 } else if (temperature[j] > T.mortality[4] && temperature[j] <= T.mortality[5]) { 275 temperature[j] * slopes[4] + intercepts[4];
276 temperature[j] * slopes[4] + intercepts[4]; 276 } else if (temperature[j] > T.mortality[5] && temperature[j] <= T.mortality[6]) {
277 } else if (temperature[j] > T.mortality[5] && temperature[j] <= T.mortality[6]) { 277 temperature[j] * slopes[5] + intercepts[5];
278 temperature[j] * slopes[5] + intercepts[5]; 278 } else if (temperature[j] > T.mortality[6] && temperature[j] <= T.mortality[7]) {
279 } else if (temperature[j] > T.mortality[6] && temperature[j] <= T.mortality[7]) { 279 temperature[j] * slopes[6] + intercepts[6];
280 temperature[j] * slopes[6] + intercepts[6]; 280 } else if (temperature[j] > T.mortality[7]) {
281 } else if (temperature[j] > T.mortality[7]) { 281 temperature[j] * slopes[7] + intercepts[7];
282 temperature[j] * slopes[7] + intercepts[7]; 282 }
283 } 283 # If mortality > 100, make it equal to 100.
284 # If mortality > 100, make it equal to 100.
285 mortality.probability[mortality.probability>100] = 100;
286 # If mortality <0, make equal to 0.
287 mortality.probability[mortality.probability<0] = 0;
288 }
289 } else {
290 # Make mortality adjustments based on adj parameter.
291 mortality.probability = (100 - mortality.probability) * adj + mortality.probability;
292 # if mortality > 100, make it equal to 100.
293 mortality.probability[mortality.probability>100] = 100; 284 mortality.probability[mortality.probability>100] = 100;
294 # If mortality <0, make equal to 0. 285 # If mortality <0, make equal to 0.
295 mortality.probability[mortality.probability<0] = 0; 286 mortality.probability[mortality.probability<0] = 0;
296 # Change percent to proportion. 287 }
297 mortality.probability = mortality.probability / 100; 288 # Make mortality adjustments based on adj parameter.
298 } 289 mortality.probability = (100 - mortality.probability) * adj + mortality.probability;
290 # if mortality > 100, make it equal to 100.
291 mortality.probability[mortality.probability>100] = 100;
292 # If mortality <0, make equal to 0.
293 mortality.probability[mortality.probability<0] = 0;
294 # Change percent to proportion.
295 mortality.probability = mortality.probability / 100;
296 }
299 return(mortality.probability) 297 return(mortality.probability)
300 } 298 }
301 299
302 mortality.nymph = function(temperature) { 300 mortality.nymph = function(temperature) {
303 if (temperature < 12.7) { 301 if (temperature < 12.7) {