Generate_VIMC_Burden_Dataset
Generate_VIMC_Burden_Dataset.RdGenerate annual burden data in format used by VIMC
Usage
Generate_VIMC_Burden_Dataset(
FOI_values = c(),
R0_values = c(),
input_data = list(),
template = NULL,
vaccine_efficacy = 1,
time_inc = 1,
mode_start = 1,
start_SEIRV = NULL,
mode_time = 0,
n_reps = 1,
deterministic = FALSE,
p_severe_inf = 0.12,
p_death_severe_inf = 0.39,
p_rep_severe = 1,
p_rep_death = 1,
YLD_per_case = 0.006486,
mode_parallel = FALSE,
cluster = NULL,
seed = NULL
)Arguments
- FOI_values
Array of values of force of infection due to spillover from sylvatic reservoir by region + time point
- R0_values
Array of values of basic reproduction number for human-human transmission by region and time point
- input_data
List of population and vaccination data for multiple regions
- template
Burden data in VIMC format, with regions, years, minimum and maximum age, and life expectancy for each line
- vaccine_efficacy
Fractional vaccine efficacy
- time_inc
Time increment in days to use in model (should be either 1.0, 2.5 or 5.0 days)
- 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 (stratified by age)
If mode_start = 2, use SEIRV input in list from previous run(s)- start_SEIRV
SEIRV data from end of a previous run to use as input (list of datasets, one per region)
- mode_time
Type of time dependence of FOI_spillover and R0 to be used:
If mode_time = 0, no time variation (constant values)
If mode_time = 1, FOI/R0 vary annually without seasonality (number of values = number of years to consider)
If mode_time = 2, FOI/R0 vary with monthly seasonality without inter-annual variation (number of values = 12)
If mode_time = 3, FOI/R0 vary with daily seasonality without inter-annual variation (number of values = 365/dt)
If mode_time = 4, FOI/R0 vary annually with monthly seasonality (number of values = 12*number of years to consider)
If mode_time = 5, FOI/R0 vary annually with daily seasonality (number of values = (365/dt)*number of years to consider)- n_reps
number of stochastic repetitions
- deterministic
TRUE/FALSE - set model to run in deterministic mode if TRUE
- p_severe_inf
Probability of an infection being severe
- p_death_severe_inf
Probability of a severe infection resulting in death
- p_rep_severe
Probability of reporting of a severe but non-fatal infection
- p_rep_death
Probability of reporting of a fatal infection
- YLD_per_case
TBA
- 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 FALSE. '