Description Usage Arguments Details Value Note Author(s) References See Also Examples

This function calculate the estimated per-challenge vaccine efficacy.

1 | ```
calcVEk(object, newdata, CIlevel=0.95)
``` |

`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. |

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.

`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. |

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

Bin Yao, Ying Huang and Chaeryon Kang

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.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ```
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)
``` |

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