poems: population_transitions – R documentation

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population_transitions

Nested functions for stage-based population transitions.

Description

Modular functions for the population simulator for performing staged-based (Leslie/Lefkovitch matrix) transitions via 3D survival and fecundity arrays.

Usage

population_transitions(
  populations,
  demographic_stochasticity,
  fecundity_matrix,
  fecundity_max,
  survival_matrix
)

Arguments

`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).

Value

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.

poems

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