Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 92:fdc148a9695a draft

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author greg
date Fri, 01 Dec 2017 09:38:04 -0500
parents b6b42e12e173
children 06acadd38824
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91:b6b42e12e173 92:fdc148a9695a
211 # TODO: user definable as well? 211 # TODO: user definable as well?
212 num_insects <- 1000 212 num_insects <- 1000
213 # Generation, Stage, degree-days, T, Diapause. 213 # Generation, Stage, degree-days, T, Diapause.
214 vec.ini <- c(0, 3, 0, 0, 0) 214 vec.ini <- c(0, 3, 0, 0, 0)
215 # Overwintering, previttelogenic, degree-days=0, T=0, no-diapause. 215 # Overwintering, previttelogenic, degree-days=0, T=0, no-diapause.
216 vec.mat <- rep(vec.ini, n) 216 vec.mat <- rep(vec.ini, num_insects)
217 # Complete matrix for the population. 217 # Complete matrix for the population.
218 vec.mat <- base::t(matrix(vec.mat, nrow=5)) 218 vec.mat <- base::t(matrix(vec.mat, nrow=5))
219 # Time series of population size. 219 # Time series of population size.
220 tot.pop <- NULL 220 tot.pop <- NULL
221 gen0.pop <- rep(0, opt$num_days) 221 gen0.pop <- rep(0, opt$num_days)
238 # Trash bin for death. 238 # Trash bin for death.
239 death.vec <- NULL 239 death.vec <- NULL
240 # Newborn. 240 # Newborn.
241 birth.vec <- NULL 241 birth.vec <- NULL
242 # All individuals. 242 # All individuals.
243 for (i in 1:n) { 243 for (i in 1:num_insects) {
244 # Find individual record. 244 # Find individual record.
245 vec.ind <- vec.mat[i,] 245 vec.ind <- vec.mat[i,]
246 # First of all, still alive? 246 # First of all, still alive?
247 # Adjustment for late season mortality rate. 247 # Adjustment for late season mortality rate.
248 if (latitude < 40.0) { 248 if (latitude < 40.0) {
455 vec.mat <- rbind(vec.mat, birth.vec) 455 vec.mat <- rbind(vec.mat, birth.vec)
456 # Update population size for the next day. 456 # Update population size for the next day.
457 num_insects <- num_insects - num_insects.death + num_insects.newborn 457 num_insects <- num_insects - num_insects.death + num_insects.newborn
458 458
459 # Aggregate results by day. 459 # Aggregate results by day.
460 tot.pop <- c(tot.pop, n) 460 tot.pop <- c(tot.pop, num_insects)
461 # Egg. 461 # Egg.
462 s0 <- sum(vec.mat[,2] == 0) 462 s0 <- sum(vec.mat[,2] == 0)
463 # Young nymph. 463 # Young nymph.
464 s1 <- sum(vec.mat[,2] == 1) 464 s1 <- sum(vec.mat[,2] == 1)
465 # Old nymph. 465 # Old nymph.