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"
)