kyotil (version 2016.11-9)

VEplot: Vaccine Efficacy Plots

Description

Vaccine efficacy plots.

Usage

VEplot (object, ...)  
"VEplot" (object, resid = TRUE, se = TRUE, df = 4, nsmo = 40,  var, ylab="VE", xlab="Time", ...) 
myplot.cox.zph (x, resid = TRUE, se = TRUE, df = 4, nsmo = 40, var,  coef.transform=NULL,  ylab=NULL,  xlab="Time",  ...)

Arguments

object

An object

x

An object of type cox.zph

resid

Boolean, whether to plot residuals

se

Boolean, whether to plot confidence band

df

degrees of freedom

nsmo

number of points used to plot the fitted spline

var

estimated variance matrix from the Cox model fit

xlab

x label

ylab

y label

coef.transform

a function to transform Cox hazard ratio estimate

...

additional parameters

Details

VEplot and myplot.cox.zph are extensions of survival::plot.cox.zph to plot VE curve and other transformations.

myplot.cox.zph adds the following parameters to the original list of parameters in plot.cox.zph: coef.transform: a function to transform the coefficients ylab: y axis label xlab: x axis label

References

Durham, L. Kathryn, et al. "Estimation of vaccine efficacy in the presence of waning: application to cholera vaccines." American Journal of Epidemiology 147.10 (1998): 948-959.

Examples

library(survival)
vfit <- coxph(Surv(time,status) ~ trt + factor(celltype) + 
              karno + age, data=veteran, x=TRUE) 
temp <- cox.zph(vfit) 

par(mfrow=c(2,2))
for (v in c("trt","age")) {
    VEplot(temp, var=v, resid=FALSE, main=v, ylab="VE")
    plot(temp, var=v, resid=FALSE, main=v)
}