thylacine_example_metrics_rerun

A dataset containing precalculated (re-run) summary metrics for use when running the
Thylacine example vignette in demonstration mode. The values were obtained by running
the vignette code for 10 replicate re-runs of the selected 'best' 200 model
simulations with <code>DEMONSTRATION = FALSE</code>.

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_metrics_rerun function

A data frame with 2,000 rows and 4 variables:<dl>
<dt>index</dt>
<dd>Example simulation number from 1 to 2,000</dd><dt>bounty_slope_error</dt>
<dd>Root mean squared error (RMSE) from estimated total bounty submitted across three intervals (see vignette)</dd><dt>ibra_extirpation_error</dt>
<dd>RMSE from estimated extirpation date for each IBRA bioregion (see vignette)</dd><dt>total_extinction</dt>
<dd>Total extinction date for each example simulation (<code>NA</code> when persistent beyond 1967)</dd>
</dl>

Format

Thylacine vignette demonstration example (re-run) metrics — thylacine_example_metrics_rerun

A data frame with 2,000 rows and 4 variables:<dl>
<dt>index</dt>
<dd>Example simulation number from 1 to 2,000</dd>

<dt>bounty_slope_error</dt>
<dd>Root mean squared error (RMSE) from estimated total bounty submitted across three intervals (see vignette)</dd>

<dt>ibra_extirpation_error</dt>
<dd>RMSE from estimated extirpation date for each IBRA bioregion (see vignette)</dd>

<dt>total_extinction</dt>
<dd>Total extinction date for each example simulation (<code>NA</code> when persistent beyond 1967)</dd>


</dl>

thylacine_example_metrics_rerun: Thylacine vignette demonstration example (re-run) metrics

Description

Arguments

Format

Examples