disease_results {epizootic} | R Documentation |
Modular functions for the disease simulator for initializing, calculating and collecting simulator results.
disease_results(
replicates,
time_steps,
seasons,
stages,
compartments,
coordinates,
initial_abundance,
results_selection = NULL,
results_breakdown = NULL
)
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. |
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.