View source: R/population_env_stoch.R
population_env_stoch | R Documentation |
Modular functions for the population simulator for performing correlated environmentally stochastic adjustments to transition rates.
population_env_stoch(
populations,
fecundity_matrix,
fecundity_max,
survival_matrix,
standard_deviation,
correlation
)
populations |
Number of populations. |
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). |
standard_deviation |
Standard deviation matrix for applying environmental stochasticity to transition rates. |
correlation |
List containing either an environmental correlation matrix (correlation_matrix), a pre-calculated transposed (Cholesky) decomposition matrix (t_decomposition_matrix), or a compact transposed (Cholesky) decomposition matrix (t_decomposition_compact_matrix) and a corresponding map of population indices (t_decomposition_compact_map), as per SpatialCorrelation class attributes. |
Environmental stochasticity calculation function: function(fecundity_array, survival_array, 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).
occupied_indices
Array of indices for those populations occupied.
returns
List containing stochastically varied fecundity and survival arrays.
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))
standard_deviation <- (fecundity_matrix + survival_matrix) * 0.3
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]
env_stoch_function <- population_env_stoch(
populations = 7, fecundity_matrix, fecundity_max = NULL, survival_matrix,
standard_deviation, correlation = NULL
)
env_stoch_function(fecundity_array, survival_array, occupied_indices)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.