README.md

In sachsmc/ggkm: Survival Plots for ggplot2

Calculate and Display Kaplan Meier Curves using ggplot2

Installation

This version of the package is not on CRAN. It can be installed with

install.packages("ggplot2")
devtools::install_github("sachsmc/ggkm")

Basic usage

library(ggkm)

## Loading required package: ggplot2

## Loading required package: survival

## Loading required package: scales

ggplot(lung, aes(time = time, status = status)) + geom_km()

ggplot(lung, aes(time = time, status = status)) + geom_km() + facet_wrap(~ sex)

ggplot(lung, aes(time = time, status = status, color = factor(sex))) + geom_km()

Adding Tick marks

Tick marks are displayed at censoring times that are also not event times

ggplot(lung, aes(time = time, status = status)) + geom_km() + geom_kmticks()

ggplot(lung, aes(time = time, status = status)) + geom_km() + geom_kmticks(shape = 1)

ggplot(lung, aes(time = time, status = status)) + geom_km() + geom_kmticks(shape = "|")

ggplot(lung, aes(time = time, status = status)) + geom_km() + geom_kmticks(shape = "|", size = 5)

Adding confidence bands

ggplot(lung, aes(time = time, status = status, color = factor(sex))) + geom_km() + geom_kmband()

ggplot(lung, aes(time = time, status = status, fill = factor(sex), color = factor(sex))) + geom_km() + geom_kmband()

ggplot(lung, aes(time = time, status = status, color = factor(sex))) + geom_km() + geom_kmband(conf.int = .99)

ggplot(lung, aes(time = time, status = status)) + geom_km() + geom_kmband(conf.int = .99) + facet_wrap(~ sex, labeller = "label_both")

Tranformations

ggplot(lung, aes(time = time, status = status)) + geom_km(trans = "cumhaz") + 
  geom_kmticks(trans = "cumhaz") + geom_kmband(trans = "cumhaz") + ylab("Cumulative hazard")

ggplot(lung, aes(time = time, status = status)) + geom_km(trans = "event") + 
  geom_kmticks(trans = "event") + geom_kmband(trans = "event") + ylab("Cumulative Events (CDF)")

## proportional hazards -> parallel lines on cloglog scale
ggplot(lung, aes(time = time, status = status, color = factor(sex))) + geom_km(trans = "cloglog") + 
  geom_kmticks(trans = "cloglog") + geom_kmband(trans = "cloglog") + ylab("Complementary Log-Log") + scale_x_log10()

## Warning: Transformation introduced infinite values in continuous x-axis

## Warning: Transformation introduced infinite values in continuous x-axis

Acknowledgements

This package would not be possible without the following:

• ggplot2

License

The MIT License (MIT)

Copyright (c) 2016 Michael C Sachs

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

sachsmc/ggkm documentation built on Oct. 18, 2023, 9:43 p.m.