check_aspatial_siri_inputs: Helper function to check the validity of inputs to the...

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

Helper function to check the validity of inputs to the siri_model_summer and siri_model_winter functions.

Description

This is an internal function that checks inputs to the disease_simulator function to make sure they are valid, and sets default values for needed inputs if their values are not supplied. The possible inputs for this function are the same as the possible inputs to the disease_simulator function.

Usage

check_aspatial_siri_inputs(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 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.) 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.

Value

A list identical to the inputs (if there are no errors.)

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