total_burden_estimate
total_burden_estimate.RdFunction to calculate annual yellow fever burden across multiple regions based on derived parameters
Usage
total_burden_estimate(
type = "FOI+R0 enviro",
param_dist = list(),
input_data = list(),
start_SEIRV = NULL,
years_data = c(),
n_reps = 1,
mode_start = 1,
flag_reporting = FALSE,
dt = 5,
enviro_data = NULL,
R0_fixed_values = NULL,
vaccine_efficacy = NULL,
p_rep_severe = NULL,
p_rep_death = NULL,
m_FOI_Brazil = 1
)Arguments
- type
Type of parameter set (FOI only, FOI+R0, FOI and/or R0 coefficients associated with environmental covariates); choose from "FOI","FOI+R0","FOI enviro","FOI+R0 enviro"
- param_dist
Data frame of values of input parameters, one set per row
- input_data
List of population and vaccination data for multiple regions
- start_SEIRV
SEIRV data to use as input
- years_data
Vector of years for which to output data
- n_reps
Number of repeats over which to average results
- 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)
- flag_reporting
Flag indicating whether to output number of reported severe and fatal cases
- dt
Time increment in days to use in model (should be either 1.0 or 5.0 days)
- enviro_data
enviro_data Data frame containing values of environmental covariates; set to NULL if not in use
- R0_fixed_values
Values of R0 to use if not being taken from parameter distribution
- vaccine_efficacy
Vaccine efficacy (set to NULL if being varied as a parameter)
- p_rep_severe
Probability of observation of severe infection (set to NULL if being varied as a parameter)
- p_rep_death
Probability of observation of death (set to NULL if being varied as a parameter)
- m_FOI_Brazil
Multiplier of spillover FOI for Brazil regions (set to NULL if being varied as a parameter)