poems: population_env_stoch – R documentation

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population_env_stoch

Nested functions for population environmental stochasticity.

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.

Pattern-Oriented Ensemble Modeling System

v1.0.1

GPL-3

Authors

Sean Haythorne [aut, cre], Damien Fordham [aut], Stuart Brown [aut], Jessie Buettel [aut], Barry Brook [aut]

Initial release