simPH: ggfitStrata – R documentation

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ggfitStrata

Graph fitted stratified survival curves from Cox Proportional Hazards models

Description

This function largely improves plot.survfit. It plots the curves using ggplot2 rather than base R graphics. One major advantage is the ability to split the survival curves into multiple plots and arrange them in a grid. This makes it easier to examine many strata at once. Otherwise they can be very bunched up.

Note: the strata legend labels need to be changed manually (see revalue) in the survfit object with the strata component.

Usage

ggfitStrata(
  obj,
  byStrata = FALSE,
  xlab = "",
  ylab = "",
  title = "",
  lcolour = "#2C7FB8",
  rcolour = "#2C7FB8"
)

Arguments

`obj`	a `survfit` object.
`byStrata`	logical, whether or not you want to include all of the stratified survival curves on one plot or separate them into a grid arranged plot.
`xlab`	a label for the plot's x-axis
`ylab`	a label of the plot's y-axis
`title`	plot title.
`lcolour`	line color. Currently only works if `byStrata = TRUE`. The default it `lcolour = "#2C7FB8"` (a bluish hexadecimal colour)
`rcolour`	confidence bounds ribbon color. Either a single color or a vector of colours. The default it `lcolour = "#2C7FB8"` (a bluish hexadecimal colour)

Details

ggfitStrata graphs fitted survival curves created with survfit using ggplot2.

Examples

# Load packages
library(survival)
library(simPH)

# Subset data
bladder1 <- bladder[bladder$enum < 5, ]

# Estimate coxph model (note that this model is for code illustration only)
M1 <- coxph(Surv(stop, event) ~ (rx + size + number) + strata(enum) +
                cluster(id), bladder1)

# Find predicted values
M1Fit <- survfit(M1)

# Plot strata in a grid
ggfitStrata(M1Fit, byStrata = TRUE)

# Plot all in one
ggfitStrata(M1Fit, byStrata = FALSE)

simPH

Simulate and Plot Estimates from Cox Proportional Hazards Models

v1.3.13

GPL-3

Authors

Christopher Gandrud [aut, cre]

Initial release

2021-01-09