View source: R/population_transitions.R
population_transitions | R Documentation |
Modular functions for the population simulator for performing staged-based (Leslie/Lefkovitch matrix) transitions via 3D survival and fecundity arrays.
population_transitions(
populations,
demographic_stochasticity,
fecundity_matrix,
fecundity_max,
survival_matrix
)
populations |
Number of populations. |
demographic_stochasticity |
Boolean for choosing demographic stochasticity for transitions. |
fecundity_matrix |
Matrix of transition fecundity rates (Leslie/Lefkovitch matrix with non-zero fecundities only). |
fecundity_max |
Maximum transition fecundity rate (in Leslie/Lefkovitch matrix). |
survival_matrix |
Matrix of transition survival rates (Leslie/Lefkovitch matrix with non-zero survivals only). |
Transition calculation function: function(fecundity_array, survival_array, stage_abundance, occupied_indices)
, where:
fecundity_array
3D array of fecundity rates (stages rows by stages columns by populations deep).
survival_array
3D array of survival rates (stages rows by stages columns by populations deep).
stage_abundance
Matrix of stage abundances for each population at time step (stages rows by populations columns).
occupied_indices
Array of indices for those populations occupied.
returns
Transitioned stage abundances.
# Deterministic transition (no stochasticity)
fecundity_matrix <- array(c(0, 0, 0, 3, 0, 0, 4, 0, 0), c(3, 3))
survival_matrix <- array(c(0, 0.5, 0, 0, 0, 0.7, 0, 0, 0.8), c(3, 3))
variation_array <- array(rep(seq(0.85, 1.15, 0.05), each = 9), c(3, 3, 7))
fecundity_array <- array(fecundity_matrix, c(3, 3, 7)) * variation_array
survival_array <- array(survival_matrix, c(3, 3, 7)) * variation_array
stage_abundance <- matrix(c(
7, 13, 0, 26, 0, 39, 47,
2, 0, 6, 8, 0, 12, 13,
0, 3, 4, 6, 0, 9, 10
), nrow = 3, ncol = 7, byrow = TRUE)
occupied_indices <- (1:7)[-5]
transition_function <- population_transitions(
populations = 7, demographic_stochasticity = FALSE,
fecundity_matrix = fecundity_matrix, fecundity_max = NULL,
survival_matrix = survival_matrix
)
transition_function(fecundity_array, survival_array, stage_abundance,
occupied_indices)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.