Model_Run_Split
Model_Run_Split.Rd
Run full version of SEIRV model with daily infection output split into sylvatic and urban
Arguments
- FOI_spillover
Force of infection due to spillover from sylvatic reservoir
- R0
Basic reproduction number for urban spread of infection
- vacc_data
Vaccination coverage in each age group by year
- pop_data
Population in each age group by year
- years_data
Incremental vector of years denoting years for which to save data
- start_SEIRV
SEIRV data from end of a previous run to use as input
- year0
First year in population/vaccination data
- mode_start
Flag indicating how to set initial population immunity level in addition to vaccination If mode_start=0, only vaccinated individuals If mode_start=1, shift some non-vaccinated individuals into recovered to give herd immunity If mode_start=2, use SEIRV input in list from previous run(s)
- vaccine_efficacy
Proportional vaccine efficacy
- dt
Time increment in days to use in model (should be 1.0, 2.5 or 5.0 days)
- n_particles
number of particles to use
- n_threads
number of threads to use
- deterministic
TRUE/FALSE - set model to run in deterministic mode if TRUE '
Details
Accepts epidemiological + population parameters and model settings; runs full version of SEIRV model for one region over a specified time period for a number of particles/threads and outputs time-dependent SEIRV values, infection numbers and total force of infection values. Daily infection output split into sylvatic and urban.