stat_kmticks: Adds tick marks to a Kaplan Meier Estimate of Survival

Description Usage Arguments Details Value Aesthetics See Also Examples

View source: R/ggkm.R

Description

Adds tick marks to a Kaplan Meier Estimate of Survival

Usage

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stat_kmticks(
  mapping = NULL,
  data = NULL,
  geom = "kmticks",
  position = "identity",
  show.legend = NA,
  inherit.aes = TRUE,
  trans,
  ...
)

Arguments

mapping

Set of aesthetic mappings created by aes() or aes_(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

data

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

geom

The geometric object to use display the data

position

Position adjustment, either as a string, or the result of a call to a position adjustment function.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

trans

Transformation to apply to the survival probabilities. Defaults to "identity". Other options include "event", "cumhaz", "cloglog", or define your own using trans_new.

...

Other arguments passed to survfit.formula

Details

This stat is for computing the tick marks for a Kaplan-Meier survival estimate for right-censored data. The tick marks will appear at each censoring time which is also not a death time, which is the default for plot.survfit. It requires the aesthetic mapping x for the observation times and status which indicates the event status, normally 0=alive, 1=dead. Other choices are TRUE/FALSE (TRUE = death) or 1/2 (2=death).

Value

a data.frame with additional columns:

x

x in data

y

Kaplan-Meier Survival Estimate at x

Aesthetics

stat_kmticks understands the following aesthetics (required aesthetics are in bold):

See Also

stat_km; stat_kmband

Examples

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library(ggplot2)
sex <- rbinom(250, 1, .5)
df <- data.frame(time = exp(rnorm(250, mean = sex)), status = rbinom(250, 1, .75), sex = sex)
ggplot(df, aes(time = time, status = status, color = factor(sex))) +
 stat_km() + stat_kmticks()

ggquickeda documentation built on June 22, 2021, 5:08 p.m.