siri_model_winter: Simulate a _Mycoplasma gallisepticum_ Outbreak in the...

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

Simulate a Mycoplasma gallisepticum Outbreak in the Non-Breeding Season

Description

Simulate a Mycoplasma gallisepticum outbreak during the non-breeding season day-by-day in a population of house finches (Haemorhous mexicanus). Uses a SIRI model (Susceptible-Infected 1- Recovered-Infected 2+) and includes demographic stochasticity in fecundity, mortality, and infection.

Usage

siri_model_winter(inputs)

Arguments

inputs

A nested list with named elements: replicates Number of replicate simulation runs. time_steps Number of simulation time steps. populations Number of populations. stages Number of life cycle stages. compartments Number of disease compartments (e.g., 3 for a SIR model). abundance_threshold A quasi-extinction threshold below 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.) r Simulation replicate. tm Simulation time step. carrying_capacity Array of carrying capacity values for each population at time step. breeding_season_length Array of breeding season lengths in days for each population at time step. segment_abundance Matrix of (current) abundance for each stage-compartment combo (rows) and population (columns) at time step. occupied_indices Array of indices for populations occupied at (current) time step. simulator poems::SimulatorReference object with dynamically accessible attached and results lists. additional attributes Additional attributes when the transformation is optionally nested in a list.

Details

The function can also handle the case in which there are no infected individuals. The principal difference between this function and the one for simulating an outbreak in the breeding season is that this one does not include fecundity.

Value

An abundance matrix with populations columns and stages*compartments rows, updated from the segment_abundance input in inputs according to demography and disease dynamics.

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