DiseaseModel.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/DiseaseModel.R
\name{DiseaseModel}
\alias{DiseaseModel}
\title{R6 class representing a disease model of the \emph{Mycoplasma gallisepticum}
outbreak in \emph{Haemorhous mexicanus}}
\description{
A \code{\link[R6:R6Class]{R6::R6Class}} class representing fixed settings
for a spatially-explicit demographic-based SIRI model of disease dynamics. It
extends the \code{\link[poems:SimulationModel]{poems::SimulationModel}} class with parameters for the
\code{\link{disease_simulator}} function. It inherits functionality for
creating a nested model, whereby a nested template model with fixed
parameters is maintained when a model is cloned for various sampled
parameters. Also provided are extensions to the methods for checking the
consistency and completeness of model parameters.
}
\section{Super classes}{
\code{\link[poems:GenericClass]{poems::GenericClass}} -> \code{\link[poems:GenericModel]{poems::GenericModel}} -> \code{\link[poems:SpatialModel]{poems::SpatialModel}} -> \code{\link[poems:SimulationModel]{poems::SimulationModel}} -> \code{DiseaseModel}
}
\section{Public fields}{
\if{html}{\out{<div class="r6-fields">}}
\describe{
\item{\code{attached}}{A list of dynamically attached attributes (name-value
pairs).}
}
\if{html}{\out{</div>}}
}
\section{Active bindings}{
\if{html}{\out{<div class="r6-active-bindings">}}
\describe{
\item{\code{simulation_function}}{Name (character string) or source path of the
default simulation function, which takes a model as an input and
returns the simulation results.}

\item{\code{model_attributes}}{A vector of model attribute names.}

\item{\code{region}}{A \code{\link[poems:Region]{poems::Region}} (or inherited class) object specifying
the study region.}

\item{\code{coordinates}}{Data frame (or matrix) of X-Y population (WGS84)
coordinates in longitude (degrees West) and latitude (degrees North)
(get and set), or distance-based coordinates dynamically returned by
region raster (get only).}

\item{\code{random_seed}}{Number to seed the random number generation for
stochasticity.}

\item{\code{replicates}}{Number of replicate simulation runs.}

\item{\code{time_steps}}{Number of simulation time steps.}

\item{\code{years_per_step}}{Number of years per time step.}

\item{\code{populations}}{Number of population cells.}

\item{\code{initial_abundance}}{Array (matrix) or raster (stack) of initial
abundance values at each population cell (for each age/stage).}

\item{\code{demographic_stochasticity}}{Boolean for choosing demographic
stochasticity for transition, dispersal, harvest and/or other processes.}

\item{\code{standard_deviation}}{Standard deviation matrix (or single value) for
applying environmental stochasticity to transition rates.}

\item{\code{correlation}}{Simulator-dependent attribute or list of attributes
for describing/parameterizing the correlation strategy utilized when
applying environmental stochasticity and/or other processes (see
\code{\link[poems:population_simulator]{poems::population_simulator}}).}

\item{\code{stages}}{Number of life cycle stages (default 1).}

\item{\code{compartments}}{Number of disease compartments (default 1).}

\item{\code{results_breakdown}}{A string with one of these values: "segments" (default),
"compartments", "stages" or "pooled." "segments" returns results for each
segment (stage x compartment combination.) "compartments" returns results for
each disease compartment. "stages" returns results for each life cycle stage.
"pooled" returns results that are not broken down by stage or compartment.}

\item{\code{carrying_capacity}}{Array (matrix), or raster (stack) of carrying
capacity values at each population cell (across time).}

\item{\code{density_dependence}}{Simulator-dependent function, attribute or list
of attributes for describing/parameterizing the density dependence
strategy utilized (see \code{\link[poems:population_simulator]{poems::population_simulator}}).}

\item{\code{growth_rate_max}}{Maximum growth rate (utilized by density
dependence processes).}

\item{\code{fecundity}}{A vector of fecundity rates, one for each combination of
stages and compartments for which fecundity applies (see
\code{fecundity_mask} below). If fecundity varies among seasons, a list
of fecundity vectors with the same length as \code{seasons} may be
provided. Required input.}

\item{\code{density_stages}}{Array of booleans or numeric (0-1) for each stage
to indicate (the degree to) which stages are affected by density
(default is 1 for all stages).}

\item{\code{translocation}}{Simulator-dependent function, attribute or list of
attributes for describing/parameterizing translocation (management)
strategies utilized (see \code{\link[poems:population_simulator]{poems::population_simulator}}).}

\item{\code{harvest}}{Simulator-dependent function, attribute or list of
attributes for describing/parameterizing a harvest (organism
removal/hunting) strategy (see \code{\link[poems:population_simulator]{poems::population_simulator}}).}

\item{\code{mortality}}{Simulator-dependent function, attribute or list of
attributes to describe/parameterize a spatio-temporal mortality
strategy (see \code{\link[poems:population_simulator]{poems::population_simulator}}).}

\item{\code{dispersal}}{Simulator-dependent function, attribute or list of
attributes for describing/parameterizing the dispersal (migration)
strategy utilized (see \code{\link{disease_simulator}}).}

\item{\code{dispersal_stages}}{Array of relative dispersal (0-1) for each stage
to indicate the degree to which each stage participates in dispersal
(default is 1 for all stages).}

\item{\code{dispersal_source_n_k}}{Simulator-dependent attribute for
describing/parameterizing dispersal dependent on source population
abundance divided by carrying capacity (see
\code{\link{disease_simulator}}).}

\item{\code{dispersal_target_k}}{Simulator-dependent attribute for
describing/parameterizing dispersal dependent on target population
carrying capacity (see \code{\link{disease_simulator}}).}

\item{\code{dispersal_target_n}}{Simulator-dependent attribute (default is list
with \emph{threshold} and \emph{cutoff}) of attributes for
describing/parameterizing dispersal dependent on target population
abundance (see \code{\link{disease_simulator}}).}

\item{\code{dispersal_target_n_k}}{Simulator-dependent attribute (default is
list with \emph{threshold} and \emph{cutoff}) of attributes for
describing/parameterizing dispersal dependent on target population
abundance/capacity (see \code{\link[poems:population_simulator]{poems::population_simulator}}).}

\item{\code{abundance_threshold}}{Abundance threshold (that needs to be
exceeded) for each population to persist.}

\item{\code{seasons}}{Number of seasons in a year (default 1.) The first one is
always treated as the breeding season.}

\item{\code{simulation_order}}{A vector of simulation process names in
configured order of execution.}

\item{\code{results_selection}}{List of attributes to be included in the
returned results of each simulation run, selected from: "abundance",
"ema", "extirpation", "extinction_location", "harvested", "occupancy";
"summarize" or "replicate".}

\item{\code{attribute_aliases}}{A list of alternative alias names for model
attributes (form: \code{alias = "attribute"}) to be used with the set
and get attributes methods.}

\item{\code{template_model}}{Nested template model for fixed (non-sampled)
attributes for shallow cloning.}

\item{\code{sample_attributes}}{Vector of sample attribute names (only).}

\item{\code{required_attributes}}{Vector of required attribute names (only),
i.e. those needed to run a simulation.}

\item{\code{error_messages}}{A vector of error messages encountered when setting
model attributes.}

\item{\code{warning_messages}}{A vector of warning messages encountered when
setting model attributes.}
}
\if{html}{\out{</div>}}
}
\section{Methods}{
\subsection{Public methods}{
\itemize{
\item \href{#method-DiseaseModel-new}{\code{DiseaseModel$new()}}
\item \href{#method-DiseaseModel-set_sample_attributes}{\code{DiseaseModel$set_sample_attributes()}}
\item \href{#method-DiseaseModel-list_consistency}{\code{DiseaseModel$list_consistency()}}
\item \href{#method-DiseaseModel-clone}{\code{DiseaseModel$clone()}}
}
}
\if{html}{\out{
<details><summary>Inherited methods</summary>
<ul>
<li><span class="pkg-link" data-pkg="poems" data-topic="GenericModel" data-id="get_attribute"><a href='../../poems/html/GenericModel.html#method-GenericModel-get_attribute'><code>poems::GenericModel$get_attribute()</code></a></span></li>
<li><span class="pkg-link" data-pkg="poems" data-topic="GenericModel" data-id="get_attribute_aliases"><a href='../../poems/html/GenericModel.html#method-GenericModel-get_attribute_aliases'><code>poems::GenericModel$get_attribute_aliases()</code></a></span></li>
<li><span class="pkg-link" data-pkg="poems" data-topic="SimulationModel" data-id="get_attribute_names"><a href='../../poems/html/SimulationModel.html#method-SimulationModel-get_attribute_names'><code>poems::SimulationModel$get_attribute_names()</code></a></span></li>
<li><span class="pkg-link" data-pkg="poems" data-topic="SimulationModel" data-id="get_attributes"><a href='../../poems/html/SimulationModel.html#method-SimulationModel-get_attributes'><code>poems::SimulationModel$get_attributes()</code></a></span></li>
<li><span class="pkg-link" data-pkg="poems" data-topic="SimulationModel" data-id="incomplete_attributes"><a href='../../poems/html/SimulationModel.html#method-SimulationModel-incomplete_attributes'><code>poems::SimulationModel$incomplete_attributes()</code></a></span></li>
<li><span class="pkg-link" data-pkg="poems" data-topic="SimulationModel" data-id="inconsistent_attributes"><a href='../../poems/html/SimulationModel.html#method-SimulationModel-inconsistent_attributes'><code>poems::SimulationModel$inconsistent_attributes()</code></a></span></li>
<li><span class="pkg-link" data-pkg="poems" data-topic="SimulationModel" data-id="is_complete"><a href='../../poems/html/SimulationModel.html#method-SimulationModel-is_complete'><code>poems::SimulationModel$is_complete()</code></a></span></li>
<li><span class="pkg-link" data-pkg="poems" data-topic="SimulationModel" data-id="is_consistent"><a href='../../poems/html/SimulationModel.html#method-SimulationModel-is_consistent'><code>poems::SimulationModel$is_consistent()</code></a></span></li>
<li><span class="pkg-link" data-pkg="poems" data-topic="SimulationModel" data-id="list_completeness"><a href='../../poems/html/SimulationModel.html#method-SimulationModel-list_completeness'><code>poems::SimulationModel$list_completeness()</code></a></span></li>
<li><span class="pkg-link" data-pkg="poems" data-topic="SimulationModel" data-id="new_clone"><a href='../../poems/html/SimulationModel.html#method-SimulationModel-new_clone'><code>poems::SimulationModel$new_clone()</code></a></span></li>
<li><span class="pkg-link" data-pkg="poems" data-topic="SimulationModel" data-id="set_attributes"><a href='../../poems/html/SimulationModel.html#method-SimulationModel-set_attributes'><code>poems::SimulationModel$set_attributes()</code></a></span></li>
</ul>
</details>
}}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-DiseaseModel-new"></a>}}
\if{latex}{\out{\hypertarget{method-DiseaseModel-new}{}}}
\subsection{Method \code{new()}}{
Initialization method sets default aliases and given attributes
individually and/or from a list.
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{DiseaseModel$new(attribute_aliases = NULL, ...)}\if{html}{\out{</div>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{attribute_aliases}}{A list of alternative alias names for model
attributes (form: \code{alias = "attribute"}) to be used with the set and
get attributes methods.}

\item{\code{...}}{Parameters passed via a \emph{params} list or individually.}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-DiseaseModel-set_sample_attributes"></a>}}
\if{latex}{\out{\hypertarget{method-DiseaseModel-set_sample_attributes}{}}}
\subsection{Method \code{set_sample_attributes()}}{
Sets the names (only - when \emph{params} is a vector) and values (when
\emph{params} is a list and/or when name-value pairs are provided) of the
sample attributes for the model.
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{DiseaseModel$set_sample_attributes(params = list(), ...)}\if{html}{\out{</div>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{params}}{List of parameters/attributes (names and values) or array
of names only.}

\item{\code{...}}{Parameters/attributes passed individually.}
}
\if{html}{\out{</div>}}
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-DiseaseModel-list_consistency"></a>}}
\if{latex}{\out{\hypertarget{method-DiseaseModel-list_consistency}{}}}
\subsection{Method \code{list_consistency()}}{
Returns a boolean to indicate if (optionally selected or all) model
attributes (such as dimensions) are consistent.
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{DiseaseModel$list_consistency(params = NULL)}\if{html}{\out{</div>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{params}}{Optional array of parameter/attribute names.}
}
\if{html}{\out{</div>}}
}
\subsection{Returns}{
List of booleans (or NAs) to indicate consistency of selected/all
attributes.
}
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-DiseaseModel-clone"></a>}}
\if{latex}{\out{\hypertarget{method-DiseaseModel-clone}{}}}
\subsection{Method \code{clone()}}{
The objects of this class are cloneable with this method.
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{DiseaseModel$clone(deep = FALSE)}\if{html}{\out{</div>}}
}

\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
\item{\code{deep}}{Whether to make a deep clone.}
}
\if{html}{\out{</div>}}
}
}
}