ve function

Vaccine efficacy estimation

Calculates vaccine efficacy and confidence interval as described in Dudasova et al., 2024, BMC Med Res Methodol and Dudasova et al., 2024, NPJ Vaccines

ve(Fit, Data, nboot = 2000)

Arguments

• Fit: an object of class inheriting from "glm" or "coxph" representing the fitted model
• Data: a data frame containing the variables in the fitted model; data must include a column called "vaccine" with binary indicator of vaccination status
• nboot: a numeric value for number of bootstrap samples for confidence interval construction

Returns

a value of vaccine efficacy VE and lower and upper bound of confidence interval CI

Examples

#' # Load required packages
library(survival)

# Load an example dataset
data(data_temp)

# Fit logistic model relating neutralizing titer to disease status
logisticFit <- glm(disease_any ~ nAb1, data = data_temp, family = binomial())

# Fit Cox proportional hazards model relating neutralizing titer 
# to time to disease or end of follow-up
coxFit <- coxph(Surv(time_event, disease_any) ~ nAb1, data = data_temp)

# Estimate vaccine efficacy and 95\% confidence interval based on the fitted models
ve(logisticFit, data_temp, nboot = 500)
ve(coxFit, data_temp, nboot = 500)