aspatial_siri {epizootic}R Documentation

Helper Function for Seasonal SIRI Simulation

Description

This function is an internal one that does the aspatial simulations within one population for one timestep, for any given season.

Usage

aspatial_siri(
  initial_pop,
  season_length,
  mortality,
  transmission,
  recovery,
  fecundity,
  abundance_threshold,
  carrying_capacity,
  season
)

Arguments

initial_pop

A vector of length 8 showing the initial abundance for each combination of stage and compartment.

season_length

The length of the season in days.

mortality

A vector of length 8 with the mortality rates for each stage and compartment in the season in question.

transmission

A vector of length 8 with the transmission rates for each stage in the season in question.

recovery

A vector of length 8 with the recovery rates for each infected stage in the season in question.

fecundity

A vector of length 8 with the fecundity for each reproductive segment.

abundance_threshold

A quasi-extinction threshold below which a population becomes extinct.

carrying_capacity

A single numeric that indicates the carrying capacity of the population in this season.

season

Either "breeding" or "non-breeding."

Value

A vector of length 8 showing the abundance for each combination of stage and compartment at the end of the season.

Examples

aspatial_siri(
 initial_pop = c(50000, 50000, 0, 1, 0, 0, 0, 0),
 season_length = 100,
 mortality = c(0.004, 0, 0.00505, 0.00105, 0.004, 0, 0.0045, 5e-04),
 fecundity = c(0, 15/182, 0, 15/182, 0, 15/182, 0, 15/182),
 transmission = c(0.00002, 0.00001, 0, 0, 7.84e-06, 3.92e-06, 0, 0),
 recovery = c(0, 0, 0.05714286, 0.05714286, 0, 0, 0.1, 0.1),
 carrying_capacity = 150000,
 abundance_threshold = 10,
 season = "breeding"
)

[Package epizootic version 1.0.0 Index]