stat_kmticks: Compute locations for tick marks

In sachsmc/ggkm: Survival Plots for ggplot2

Compute locations for tick marks

Description

Tick marks are plotted where there are censoring times that are also not event times

Usage

StatKmticks

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 survival::survfit.formula

Format

An object of class StatKmticks (inherits from Stat, ggproto, gg) of length 4.

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):

• time The survival times

• status The censoring indicator, see Surv for more information.

• alpha

• color

• linetype

• size

See Also

stat_km

Examples

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()

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