disease_results {epizootic}R Documentation

Nested functions for initializing, calculating and collecting disease simulator results.

Description

Modular functions for the disease simulator for initializing, calculating and collecting simulator results.

Usage

disease_results(
  replicates,
  time_steps,
  seasons,
  stages,
  compartments,
  coordinates,
  initial_abundance,
  results_selection = NULL,
  results_breakdown = NULL
)

Arguments

replicates

Number of replicate simulation runs.

time_steps

Number of simulation time steps.

seasons

Number of seasons per time step.

stages

Number of life cycle stages.

compartments

Number of disease compartments.

coordinates

Data frame (or matrix) of X-Y population coordinates.

initial_abundance

Matrix of initial abundances at each combination of stage and compartment (in rows) for each population (in columns).

results_selection

List of results selection from: "abundance" (default), "ema", "extirpation", "extinction_location", "harvested", "occupancy"; "summarize" (default) or "replicate". "summarize" calculates mean, sd, min and max across replicates. "replicate" returns results separately for each replicate.

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.

Value

List of result functions:

initialize_attributes = function())

Constructs and returns an initialized nested list for the selected result attributes.

initialize_replicate = function(results)

Initializes and returns nested result attributes at the start of each replicate.

calculate_at_season = function(r, tm, season, segment_abundance, harvested, results)

Appends and calculates (non-NULL) results and returns nested result attributes at the end of each season within time step (tm) within replicate (r).

calculate_at_timestep = function(r, tm, segment_abundance, harvested, results)

Appends and calculates (non-NULL) results and returns nested result attributes at the end of each time step (tm) within replicate (r).

finalize_attributes = function(results)

Finalizes result calculations at the end of the simulation.


[Package epizootic version 1.0.0 Index]