disease_transformation: Nested functions for a user-defined transformation of a...

In epizootic: Spatially Explicit Population Models of Disease Transmission in Wildlife

Nested functions for a user-defined transformation of a population affected by a disease outbreak.

Description

Modular functions for the disease simulator for performing a transformation of a population across stages and disease compartments (and optionally carrying capacity) at a specified time step via a user-defined function.

Usage

disease_transformation(params)

Arguments

params

A list of parameters, which must contain all of the below, except name, which is optional: 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 populations. seasons Number of seasons per year. stages Number of life cycle stages. compartments Number of disease compartments (e.g., 3 for a SIR model). demographic_stochasticity Boolean for optionally choosing demographic stochasticity for the transformation. density_stages Array of booleans or numeric (0,1) for each stage to indicate which stages are affected by density. abundance_threshold A quasi-extinction threshold at which a population becomes extinct. mortality A vector of mortality rates, one for each combination of stages and compartments. mortality_unit A vector indicating whether mortality rates are daily or seasonal. 1 indicates seasonal, 0 indicates daily. fecundity A vector of fecundity rates, one for each combination of stages and compartments for which fecundity applies. fecundity_unit A vector indicating whether fecundity rates are daily or seasonal. 1 indicates seasonal, 0 indicates daily. fecundity_mask A vector indicating which stages and compartments reproduce. transmission A vector of transmission rates, one for each combination of stages and compartment for which transmission applies (see transmission_mask below. transmission_unit A vector indicating whether mortality rates are daily or seasonal. 1 indicates seasonal, 0 indicates daily. transmission_mask A vector indicating which stages and compartments are subject to transmission (i.e., classes susceptible to infection.) recovery A vector of recovery rates, one for each combination of stages and compartment for which recovery applies (see recovery_mask below.) recovery_unit A vector indicating whether mortality rates are daily or seasonal. 1 indicates seasonal, 0 indicates daily. recovery_mask A vector indicating which compartments are subject to recovery (i.e., infected classes that can recover.) transformation A user-defined function (optionally nested in a list with additional attributes) for performing transformation using params as arguments. simulator poems::SimulatorReference object with dynamically accessible attached and results lists. name Optional name for the transformation function. additional attributes Additional attributes when the transformation is optionally nested in a list.

Value

Abundance (and capacity) transformation function: function(r, tm, carrying_capacity, segment_abundance, occupied_indices), where:

r

Simulation replicate.

tm

Simulation time step.

carrying_capacity

Array of carrying capacity values for each population at time step.

segment_abundance

Matrix of abundance for each stage-compartment combo (rows) and population (columns) at time step.

occupied_indices

Array of indices for populations occupied at time step.

returns

List with transformed stage abundance matrix (and optionally carrying capacity).

epizootic documentation built on Oct. 2, 2024, 5:07 p.m.