Generate_VIMC_Burden_Dataset
Generate_VIMC_Burden_Dataset.RdGenerate annual burden data in format used by VIMC
Usage
Generate_VIMC_Burden_Dataset(
input_data = list(),
FOI_values = c(),
R0_values = c(),
template = NULL,
vaccine_efficacy = 1,
p_severe_inf = 0.12,
p_death_severe_inf = 0.39,
YLD_per_case = 0.006486,
mode_start = 1,
start_SEIRV = NULL,
dt = 1,
n_reps = 1,
deterministic = FALSE,
mode_parallel = FALSE,
cluster = NULL,
seed = NULL
)Arguments
- input_data
List of population and vaccination data for multiple regions
- FOI_values
Values for each region of the force of infection due to spillover from sylvatic reservoir
- R0_values
Values for each region of the basic reproduction number for human-human transmission
- template
Burden data in VIMC format, with regions, years, minimum and maximum age, and life expectancy for each line
- vaccine_efficacy
Fractional vaccine efficacy
- p_severe_inf
Probability of an infection being severe
- p_death_severe_inf
Probability of a severe infection resulting in death
- YLD_per_case
TBA
- 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 (uniform by age, R0 based only) If mode_start=2, use SEIRV input in list from previous run(s) If mode_start=3, shift some non-vaccinated individuals into recovered to give herd immunity (stratified by age)
- start_SEIRV
SEIRV data from end of a previous run to use as input (list of datasets, one per region)
- dt
Time increment in days to use in model (should be either 1.0 or 5.0 days)
- n_reps
number of stochastic repetitions
- deterministic
TRUE/FALSE - set model to run in deterministic mode if TRUE
- mode_parallel
TRUE/FALSE - set model to run in parallel using cluster if TRUE
- cluster
Cluster of threads to use if mode_parallel=TRUE
- seed
Optional random seed value to set before running each region for stochastic normalization; set to NULL to omit; will not work if mode_parallel is not set to "none". '