Mercurial > repos > greg > insect_phenology_model

comparison insect_phenology_model.R @ 101:691b677d8f83 draft

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author greg
date Mon, 04 Dec 2017 13:34:28 -0500
parents 52114847afff
children ce996e90f5a7
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100:52114847afff 101:691b677d8f83
229 # Overwintering, previttelogenic, degree-days=0, T=0, no-diapause. 229 # Overwintering, previttelogenic, degree-days=0, T=0, no-diapause.
230 vector.matrix <- rep(vector.ini, num_insects) 230 vector.matrix <- rep(vector.ini, num_insects)
231 # Complete matrix for the population. 231 # Complete matrix for the population.
232 vector.matrix <- base::t(matrix(vector.matrix, nrow=5)) 232 vector.matrix <- base::t(matrix(vector.matrix, nrow=5))
233 # Time series of population size. 233 # Time series of population size.
234 tot.pop <- NULL 234 total.population <- NULL
235 gen0.pop <- rep(0, opt$num_days) 235 overwintering_adult.population <- rep(0, opt$num_days)
236 gen1.pop <- rep(0, opt$num_days) 236 first_generation.population <- rep(0, opt$num_days)
237 gen2.pop <- rep(0, opt$num_days) 237 second_generation.population <- rep(0, opt$num_days)
238 S0 <- rep(0, opt$num_days) 238 S0 <- rep(0, opt$num_days)
239 S1 <- rep(0, opt$num_days) 239 S1 <- rep(0, opt$num_days)
240 S2 <- rep(0, opt$num_days) 240 S2 <- rep(0, opt$num_days)
241 S3 <- rep(0, opt$num_days) 241 S3 <- rep(0, opt$num_days)
242 S4 <- rep(0, opt$num_days) 242 S4 <- rep(0, opt$num_days)
478 vector.matrix <- rbind(vector.matrix, birth.vector) 478 vector.matrix <- rbind(vector.matrix, birth.vector)
479 # Update population size for the next day. 479 # Update population size for the next day.
480 num_insects <- num_insects - num_insects.death + num_insects.newborn 480 num_insects <- num_insects - num_insects.death + num_insects.newborn
481 481
482 # Aggregate results by day. 482 # Aggregate results by day.
483 tot.pop <- c(tot.pop, num_insects) 483 total.population <- c(total.population, num_insects)
484 484
485 # All adults population size. 485 # All adults population size.
486 num_insects.adult <- sum(vector.matrix[,2] == 3) + sum(vector.matrix[,2] == 4) + sum(vector.matrix[,2] == 5) 486 num_insects.adult <- sum(vector.matrix[,2] == 3) + sum(vector.matrix[,2] == 4) + sum(vector.matrix[,2] == 5)
487 487
488 # Overwintering adult population size. 488 # Overwintering adult population size.
489 gen0.pop[row] <- sum(vector.matrix[,1] == 0) 489 overwintering_adult.population[row] <- sum(vector.matrix[,1] == 0)
490 # First generation population size. 490 # First generation population size.
491 gen1.pop[row] <- sum(vector.matrix[,1] == 1) 491 first_generation.population[row] <- sum(vector.matrix[,1] == 1)
492 # Second generation population size. 492 # Second generation population size.
493 gen2.pop[row] <- sum(vector.matrix[,1] == 2) 493 second_generation.population[row] <- sum(vector.matrix[,1] == 2)
494 494
495 # Egg population size. 495 # Egg population size.
496 S0[row] <- sum(vector.matrix[,2] == 0) 496 S0[row] <- sum(vector.matrix[,2]==0)
497 # Young nymph population size. 497 # Young nymph population size.
498 S1[row] <- sum(vector.matrix[,2] == 1) 498 S1[row] <- sum(vector.matrix[,2]==1)
499 # Old nymph population size. 499 # Old nymph population size.
500 S2[row] <- sum(vector.matrix[,2] == 2) 500 S2[row] <- sum(vector.matrix[,2]==2)
501 # Previtellogenic population size. 501 # Previtellogenic population size.
502 S3[row] <- sum(vector.matrix[,2] == 3) 502 S3[row] <- sum(vector.matrix[,2]==3)
503 # Vitellogenic population size. 503 # Vitellogenic population size.
504 S4[row] <- sum(vector.matrix[,2] == 4) 504 S4[row] <- sum(vector.matrix[,2]==4)
505 # Diapausing population size. 505 # Diapausing population size.
506 S5[row] <- sum(vector.matrix[,2] == 5) 506 S5[row] <- sum(vector.matrix[,2]==5)
507 507
508 P.adult[row] <- sum(vector.matrix[,1] == 0) 508 P.adult[row] <- sum(vector.matrix[,1]==0)
509 F1.adult[row] <- sum((vector.matrix[,1] == 1 & vector.matrix[,2] == 3) | (vector.matrix[,1] == 1 & vector.matrix[,2] == 4) | (vector.matrix[,1] == 1 & vector.matrix[,2] == 5)) 509 F1.adult[row] <- sum((vector.matrix[,1]==1 & vector.matrix[,2]==3) | (vector.matrix[,1]==1 & vector.matrix[,2]==4) | (vector.matrix[,1]==1 & vector.matrix[,2]==5))
510 F2.adult[row] <- sum((vector.matrix[,1]== 2 & vector.matrix[,2] == 3) | (vector.matrix[,1] == 2 & vector.matrix[,2] == 4) | (vector.matrix[,1] == 2 & vector.matrix[,2] == 5)) 510 F2.adult[row] <- sum((vector.matrix[,1]==2 & vector.matrix[,2]==3) | (vector.matrix[,1]==2 & vector.matrix[,2]==4) | (vector.matrix[,1]==2 & vector.matrix[,2]==5))
511 511
512 N.newborn[row] <- num_insects.newborn 512 N.newborn[row] <- num_insects.newborn
513 N.death[row] <- num_insects.death 513 N.death[row] <- num_insects.death
514 N.adult[row] <- num_insects.adult 514 N.adult[row] <- num_insects.adult
515 } # end of days specified in the input temperature data 515 } # end of days specified in the input temperature data
524 S4.replications[,N.replications] <- S4 524 S4.replications[,N.replications] <- S4
525 S5.replications[,N.replications] <- S5 525 S5.replications[,N.replications] <- S5
526 newborn.replications[,N.replications] <- N.newborn 526 newborn.replications[,N.replications] <- N.newborn
527 death.replications[,N.replications] <- N.death 527 death.replications[,N.replications] <- N.death
528 adult.replications[,N.replications] <- N.adult 528 adult.replications[,N.replications] <- N.adult
529 pop.replications[,N.replications] <- tot.pop 529 pop.replications[,N.replications] <- total.population
530 P.replications[,N.replications] <- gen0.pop 530 P.replications[,N.replications] <- overwintering_adult.population
531 F1.replications[,N.replications] <- gen1.pop 531 F1.replications[,N.replications] <- first_generation.population
532 F2.replications[,N.replications] <- gen2.pop 532 F2.replications[,N.replications] <- second_generation.population
533 P_adults.replications[,N.replications] <- P.adult 533 P_adults.replications[,N.replications] <- P.adult
534 F1_adults.replications[,N.replications] <- F1.adult 534 F1_adults.replications[,N.replications] <- F1.adult
535 F2_adults.replications[,N.replications] <- F2.adult 535 F2_adults.replications[,N.replications] <- F2.adult
536 } 536 }
537 537