epizootic (version 2.0.0)

aspatial_siri: 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
)

Value

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

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"
)