method1: Analysis methods from Tokars (2018)

In impactflu: Quantification of Population-Level Impact of Vaccination

Description

Method 1 was said to be as current. Method 3 was determined to be the least biased.

Usage

method1(init_pop_size, vaccinations, cases, ve)

method3(init_pop_size, vaccinations, cases, ve)

Arguments

init_pop_size	Integer initial population size
vaccinations	Integer vector counts of vaccinations
cases	Integer vector counts of cases
ve	Vector vaccine effectiveness. If length 1, assumed to not vary with time.

Value

A tibble with the following columns (method-dependent):

cases	Observed cases
vaccinations	Observed vaccinations
ve	Assumed vaccine effectiveness
pvac	Proportion of the starting population vaccinated
vc_lag	Vaccine coverage lagged
pops	Susceptible population
pflu	Infection risk
popn	Non-cases is absence of vaccination
cases_novac	Cases in absence of vaccination
avert	Expected number of vaccinations

References

Tokars JI, Rolfes MA, Foppa IM, Reed C. An evaluation and update of methods for estimating the number of influenza cases averted by vaccination in the United States. Vaccine. 2018;36(48):7331–7337. doi:10.1016/j.vaccine.2018.10.026

Examples

library(dplyr)

# Simulate a population
nsam <- 1e6L
ndays <- 304L
pop_tok <- sim_reference(
  init_pop_size = nsam,
  vaccinations = generate_counts(nsam, ndays, 0.55, mean = 100, sd = 50),
  cases_novac = generate_counts(nsam, ndays, 0.12, mean = 190, sd = 35),
  ve = 0.48,
  lag = 14,
  deterministic = TRUE
)

# Summarise by month
pop_tok_month <- pop_tok %>%
  mutate(
    datestamp = generate_dates(
      timepoint, lubridate::ymd("2017-08-01"), "day"
    ),
    year = lubridate::year(datestamp),
    month = lubridate::month(datestamp)
 ) %>%
 group_by(year, month) %>%
 summarise(
   vaccinations = sum(vaccinations), cases = sum(cases), ve = mean(ve)
 ) %>%
 ungroup()

# Estimate averted cases using the two different methods
m1 <- method1(
  nsam, pop_tok_month$vaccinations, pop_tok_month$cases, pop_tok_month$ve
)
m3 <- method3(
  nsam, pop_tok_month$vaccinations, pop_tok_month$cases, pop_tok_month$ve
)
sum(m1$avert)
sum(m3$avert)

impactflu documentation built on Jan. 14, 2020, 5:06 p.m.