thylacine_example_matrices

A dataset containing precalculated summary matrices for use when running the
Thylacine example vignette in demonstration mode. The values were obtained by running
the vignette code for 20,000 model simulations with <code>DEMONSTRATION = FALSE</code>.
Note that some matrices were only stored for the selected 'best' 200 models.

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

thylacine_example_matrices function

A list containing the following matrices:<dl>
<dt>extirpation</dt>
<dd>200 row by 795 column matrix of cell extirpation dates for the 'best' 200 models</dd><dt>total_bounty</dt>
<dd>200 row by 80 column matrix of bounty submitted each year for the 'best' 200 models</dd><dt>ibra_bounty</dt>
<dd>200 row by 9 column matrix of total bounty submitted each IBRA bioregion for the 'best' 200 models</dd><dt>bounty_slope</dt>
<dd>20,000 row by 3 column matrix of calculated slope of total bounty submitted across 3 intervals for each sample simulation</dd><dt>ibra_extirpation</dt>
<dd>20,000 row by 9 column matrix of extirpation dates for each IBRA bioregion for each sample simulation</dd>
</dl>

Format

Thylacine vignette demonstration example matrices — thylacine_example_matrices

A list containing the following matrices:<dl>
<dt>extirpation</dt>
<dd>200 row by 795 column matrix of cell extirpation dates for the 'best' 200 models</dd>

<dt>total_bounty</dt>
<dd>200 row by 80 column matrix of bounty submitted each year for the 'best' 200 models</dd>

<dt>ibra_bounty</dt>
<dd>200 row by 9 column matrix of total bounty submitted each IBRA bioregion for the 'best' 200 models</dd>

<dt>bounty_slope</dt>
<dd>20,000 row by 3 column matrix of calculated slope of total bounty submitted across 3 intervals for each sample simulation</dd>

<dt>ibra_extirpation</dt>
<dd>20,000 row by 9 column matrix of extirpation dates for each IBRA bioregion for each sample simulation</dd>


</dl>

thylacine_example_matrices: Thylacine vignette demonstration example matrices

Description

Arguments

Format

Examples