calcVEk: Calculate Per-Challenge Vaccine Efficacy

In rld: Analyze and Design Repeated Low-Dose Challenge Experiments

Description

This function calculate the estimated per-challenge vaccine efficacy.

Usage

calcVEk(object, newdata, CIlevel=0.95)

Arguments

object	a fitted object of class inheriting from "rld".
newdata	a data list for predicting vaccine efficacy where "contrgroup" and "refgroup" list names must be included.
CIlevel	a confidence level. The default is 0.95.

Details

Per-challenge vaccine efficacy is defined as the relative reduction in the risk of infection caused by vaccination at a particular challenge, conditional on non-infection before the challenge. Please refer to Kang et al.(2015) for more details about the formula.

Value

VE	the vaccine efficacy estimates for contrast group and reference group.
se	standard deviations of per-challenge vaccine efficacy estimates.
lwr	a vector containing the lower bound values of confidence interval for VE.
upr	a vector containing the upper bound values of confidence interval for VE.

Note

In the newdata list for vaccine efficacy prediction, users must assign variable names in the contrast group and reference group.

Author(s)

Bin Yao, Ying Huang and Chaeryon Kang

References

Kang, C., Huang, Y., and Miller, C. (2015). A discrete-time survival model with random effects for designing and analyzing repeated low-dose challenge experiments. Biostatistics, 16(2): 295-310.

See Also

calcVEt, calcpk

Examples

data(SampleData)
augdata <- transdata(data = SampleData, ndlevel = 3, nexposure = c(10, 10, 2))
fitout <- rld(formula = survival::Surv(time, delta)~factor(dose)+trt+I(I(dose==3)*trt),
              data = augdata, frailty = TRUE)

contrgroup <- 1
refgroup <- 0
predata <- list(contrgroup, refgroup)
names(predata) <- c("contrgroup", "refgroup")
names(predata$contrgroup) <- c("trt")
names(predata$refgroup) <- c("trt")

VEkout <- calcVEk(object = fitout, newdata = predata, CIlevel = 0.95)
summary(VEkout)

rld documentation built on May 2, 2019, 5:57 a.m.