convert cumulative vaccination schedule to non-cumulative ----------------------------------

convert_vac_schedule(
  vac_schedule,
  ve,
  hosp_multiplier,
  delay,
  ve_trans,
  add_child_vac = FALSE,
  child_vac_coverage = 0.75,
  child_doses_per_day = 50000,
  child_vac_start_date = "2021-09-01",
  wane = FALSE,
  k = 0.03,
  t0 = 180,
  add_extra_dates = FALSE,
  extra_end_date = "2022-03-31"
)

Arguments

vac_schedule	a data frame that the proportion of the population who receives vaccines at each time point. Rows are time points, columns are vaccine type, age group, and dose. For example, the first column is the proportion of individuals in age group 1 who receive dose 1 of the first vaccine type. The function assumes 9 age groups and four vaccine types, each with a 2-dose regimen.
ve	a named list of vaccine effectiveness against infection for each dose of each vaccine type.
hosp_multiplier	a named list of the values for the vaccine effectiveness against hospitalization for each dose of each vaccine type. Vaccine effectiveness against hospitalization is incorporated as a multiplier on the probability of being hospitalized after infection as (1 – VE_hospitalization) divided by (1-VE_infection) to account for the the inclusion of people who are never infected (and thus never hospitalized) included in the estimation of VE against hospitalization.
delay	a named list of the time to protection for each dose of each vaccine type.
ve_trans	a named list of vaccine effectiveness against transmission for each dose of each vaccine type.
add_child_vac	logical, if TRUE 5-11 year olds are vaccinated
child_vac_coverage	total vaccine coverage in 5-11 to achieve (between 0 and 1) if add_child_vac = TRUE
child_doses_per_day	the number of doses to be administered to 5-11 year olds if add_child_vac = TRUE
child_vac_start_date	character string of the date (YYYY-MM-DD format) to start vaccinating 5-11 year olds, if add_child_vac = TRUE
wane	logical, if TRUE vaccine effectiveness wanes by a logistic function parameterized by arguments k and t0.
k	logistic growth rate
t0	the time point at the midpoint of the logistic curve (where 50% waning occurs)
add_extra_dates	logical, if TRUE add extra rows to the vaccination schedule until extra_end_date
extra_end_date	character string of the date (YYYY-MM-DD format) to end the vaccination schedule (which will also be the last date of the simulation)

Value

list of vaccination rate by day and dose and weighted VE and delay to protection by day and dose