population_env_stoch

Modular functions for the population simulator for performing correlated
environmentally stochastic adjustments to transition rates.

A framework of interoperable R6 classes
(Chang, 2020, <https://CRAN.R-project.org/package=R6>) for building ensembles
of viable models via the pattern-oriented modeling (POM) approach (Grimm et al.,
2005, <doi:10.1126/science.1116681>). The package includes classes for
encapsulating and generating model parameters, and managing the POM workflow.
The workflow includes: model setup; generating model parameters via Latin
hyper-cube sampling (Iman & Conover, 1980, <doi:10.1080/03610928008827996>);
running multiple sampled model simulations; collating summary results; and
validating and selecting an ensemble of models that best match known patterns.
By default, model validation and selection utilizes an approximate Bayesian
computation (ABC) approach (Beaumont et al., 2002,
<doi:10.1093/genetics/162.4.2025>), although alternative user-defined
functionality could be employed. The package includes a spatially explicit
demographic population model simulation engine, which incorporates default
functionality for density dependence, correlated environmental stochasticity,
stage-based transitions, and distance-based dispersal. The user may customize
the simulator by defining functionality for translocations, harvesting,
mortality, and other processes, as well as defining the sequence order for the
simulator processes. The framework could also be adapted for use with other
model simulators by utilizing its extendable (inheritable) base classes.

July Pilowsky

poems

Pattern-Oriented Ensemble Modeling System

Sean Haythorne

Damien Fordham

Stuart Brown

Jessie Buettel

Barry Brook

population_env_stoch function

<dl><dt>populations</dt>
<dd>Number of populations.</dd>
<dt>fecundity_matrix</dt>
<dd>Matrix of transition fecundity rates (Leslie/Lefkovitch matrix with non-zero fecundities only).</dd>
<dt>fecundity_max</dt>
<dd>Maximum transition fecundity rate (in Leslie/Lefkovitch matrix).</dd>
<dt>survival_matrix</dt>
<dd>Matrix of transition survival rates (Leslie/Lefkovitch matrix with non-zero survivals only).</dd>
<dt>standard_deviation</dt>
<dd>Standard deviation matrix for applying environmental stochasticity to transition rates.</dd>
<dt>correlation</dt>
<dd>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.</dd></dl>

Arguments

Nested functions for population environmental stochasticity. — population_env_stoch

<dl>

<dt>populations</dt>
<dd>Number of populations.</dd>


<dt>fecundity_matrix</dt>
<dd>Matrix of transition fecundity rates (Leslie/Lefkovitch matrix with non-zero fecundities only).</dd>


<dt>fecundity_max</dt>
<dd>Maximum transition fecundity rate (in Leslie/Lefkovitch matrix).</dd>


<dt>survival_matrix</dt>
<dd>Matrix of transition survival rates (Leslie/Lefkovitch matrix with non-zero survivals only).</dd>


<dt>standard_deviation</dt>
<dd>Standard deviation matrix for applying environmental stochasticity to transition rates.</dd>


<dt>correlation</dt>
<dd>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.</dd>

</dl>

population_env_stoch: Nested functions for population environmental stochasticity.

Description

Usage

Value

Arguments