inst/tinytest/visreg-coxph.R

In pbreheny/visreg: Visualization of Regression Models

# Setup
library(survival)
library(splines)
ovarian$rx <- factor(ovarian$rx)

# Basic
fit <- coxph(Surv(futime,fustat) ~ age + rx, data=ovarian)
visreg(fit, "age")
visreg(fit, "age", type="contrast")
visreg(fit, "rx")
visreg(fit, "age", trans=exp)
visreg(fit, "age", trans=exp, ylim=c(0,20))

# Interaction
fit <- coxph(Surv(futime,fustat)~age*rx,data=ovarian)
par(mfrow=c(1,2))
visreg(fit, "age", cond=list(rx="1"), print.cond=interactive())
visreg(fit, "age", cond=list(rx="2"), print.cond=interactive())
visreg(fit,"age",by="rx")
visreg2d(fit, x="age", y="rx")

# Splines
fit <- coxph(Surv(futime, fustat) ~ ns(age, 4) + rx, data=ovarian)
par(mfrow=c(1,1))
visreg(fit, "age")
visreg(fit, "rx")
visreg(fit, "age", type="contrast")
visreg(fit, "rx", type="contrast")

# Strata
ovarian$Group <- factor(ovarian$rx)
fit <- coxph(Surv(futime,fustat) ~ age+strata(Group), data=ovarian)
visreg(fit, "age")
visreg(fit, "age", type='contrast')

# Logical
ovarian$rx <- ovarian$rx == 2
fit <- coxph(Surv(futime,fustat) ~ age + rx, data=ovarian)
visreg(fit, "age")