DiseaseModel {epizootic}R Documentation

R6 class representing a disease model of the Mycoplasma gallisepticum outbreak in Haemorhous mexicanus

Description

A R6::R6Class class representing fixed settings for a spatially-explicit demographic-based SIRI model of disease dynamics. It extends the poems::SimulationModel class with parameters for the 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.

Super classes

poems::GenericClass -> poems::GenericModel -> poems::SpatialModel -> poems::SimulationModel -> DiseaseModel

Public fields

attached

A list of dynamically attached attributes (name-value pairs).

Active bindings

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.

model_attributes

A vector of model attribute names.

region

A poems::Region (or inherited class) object specifying the study region.

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).

random_seed

Number to seed the random number generation for stochasticity.

replicates

Number of replicate simulation runs.

time_steps

Number of simulation time steps.

years_per_step

Number of years per time step.

populations

Number of population cells.

initial_abundance

Array (matrix) or raster (stack) of initial abundance values at each population cell (for each age/stage).

demographic_stochasticity

Boolean for choosing demographic stochasticity for transition, dispersal, harvest and/or other processes.

standard_deviation

Standard deviation matrix (or single value) for applying environmental stochasticity to transition rates.

correlation

Simulator-dependent attribute or list of attributes for describing/parameterizing the correlation strategy utilized when applying environmental stochasticity and/or other processes (see poems::population_simulator).

stages

Number of life cycle stages (default 1).

compartments

Number of disease compartments (default 1).

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.

carrying_capacity

Array (matrix), or raster (stack) of carrying capacity values at each population cell (across time).

density_dependence

Simulator-dependent function, attribute or list of attributes for describing/parameterizing the density dependence strategy utilized (see poems::population_simulator).

growth_rate_max

Maximum growth rate (utilized by density dependence processes).

fecundity

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

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).

translocation

Simulator-dependent function, attribute or list of attributes for describing/parameterizing translocation (management) strategies utilized (see poems::population_simulator).

harvest

Simulator-dependent function, attribute or list of attributes for describing/parameterizing a harvest (organism removal/hunting) strategy (see poems::population_simulator).

mortality

Simulator-dependent function, attribute or list of attributes to describe/parameterize a spatio-temporal mortality strategy (see poems::population_simulator).

dispersal

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

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).

dispersal_source_n_k

Simulator-dependent attribute for describing/parameterizing dispersal dependent on source population abundance divided by carrying capacity (see disease_simulator).

dispersal_target_k

Simulator-dependent attribute for describing/parameterizing dispersal dependent on target population carrying capacity (see disease_simulator).

dispersal_target_n

Simulator-dependent attribute (default is list with threshold and cutoff) of attributes for describing/parameterizing dispersal dependent on target population abundance (see disease_simulator).

dispersal_target_n_k

Simulator-dependent attribute (default is list with threshold and cutoff) of attributes for describing/parameterizing dispersal dependent on target population abundance/capacity (see poems::population_simulator).

abundance_threshold

Abundance threshold (that needs to be exceeded) for each population to persist.

seasons

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

simulation_order

A vector of simulation process names in configured order of execution.

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".

attribute_aliases

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

template_model

Nested template model for fixed (non-sampled) attributes for shallow cloning.

sample_attributes

Vector of sample attribute names (only).

required_attributes

Vector of required attribute names (only), i.e. those needed to run a simulation.

error_messages

A vector of error messages encountered when setting model attributes.

warning_messages

A vector of warning messages encountered when setting model attributes.

Methods

Public methods

Inherited methods

Method new()

Initialization method sets default aliases and given attributes individually and/or from a list.

Usage
DiseaseModel$new(attribute_aliases = NULL, ...)
Arguments
attribute_aliases

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

...

Parameters passed via a params list or individually.


Method set_sample_attributes()

Sets the names (only - when params is a vector) and values (when params is a list and/or when name-value pairs are provided) of the sample attributes for the model.

Usage
DiseaseModel$set_sample_attributes(params = list(), ...)
Arguments
params

List of parameters/attributes (names and values) or array of names only.

...

Parameters/attributes passed individually.


Method list_consistency()

Returns a boolean to indicate if (optionally selected or all) model attributes (such as dimensions) are consistent.

Usage
DiseaseModel$list_consistency(params = NULL)
Arguments
params

Optional array of parameter/attribute names.

Returns

List of booleans (or NAs) to indicate consistency of selected/all attributes.


Method clone()

The objects of this class are cloneable with this method.

Usage
DiseaseModel$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.


[Package epizootic version 1.0.0 Index]