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Plot a Discrete Survival Function as a Step Function

Source: R/geom_survival_discrete.R
geom_survival_discrete.Rd

geom_survival_discrete() renders the discrete survival function \(S(x) = 1 - F(x)\) as a right-continuous step function with horizontal segments, dashed vertical jumps, open circles at the lower limit of each jump, and closed circles at the upper limit.

Usage

geom_survival_discrete(
  mapping = NULL,
  data = NULL,
  stat = StatSurvivalDiscrete,
  position = "identity",
  ...,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  fun = NULL,
  pmf_fun = NULL,
  xlim = NULL,
  support = NULL,
  args = list(),
  open_fill = NULL,
  vert_type = "dashed",
  show_points = NULL,
  show_vert = NULL
)

StatSurvivalDiscrete

GeomSurvivalDiscrete

Format

An object of class StatSurvivalDiscrete (inherits from Stat, ggproto, gg) of length 3.

An object of class GeomSurvivalDiscrete (inherits from Geom, ggproto, gg) of length 5.

Arguments

mapping

Set of aesthetic mappings created by 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:

  • NULL (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)).

stat

The statistical transformation to use on the data for this layer. When using a geom_*() function to construct a layer, the stat argument can be used to override the default coupling between geoms and stats. The stat argument accepts the following:

  • A Stat ggproto subclass, for example StatCount.

  • A string naming the stat. To give the stat as a string, strip the function name of the stat_ prefix. For example, to use stat_count(), give the stat as "count".

  • For more information and other ways to specify the stat, see the layer stat documentation.

position

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

  • The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.

  • A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter".

  • For more information and other ways to specify the position, see the layer position documentation.

...

Other parameters passed on to ggplot2::layer().

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

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. To include legend keys for all levels, even when no data exists, use TRUE. If NA, all levels are shown in legend, but unobserved levels are omitted.

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. annotation_borders().

fun

A discrete CDF function (e.g. pbinom). \(S(x) = 1 - F(x)\) is computed directly from this function on the integer support. Exactly one of fun or pmf_fun must be provided.

pmf_fun

A PMF function (e.g. dbinom). The survival function is derived as \(1 - \mathrm{cumsum}(\mathrm{pmf})\). Exactly one of fun or pmf_fun must be provided.

xlim

A numeric vector of length 2 specifying the range of integer support values.

support

An optional integer or numeric vector giving the exact support points to evaluate. When supplied, xlim is ignored.

args

A named list of additional arguments to pass to fun or pmf_fun.

open_fill

Fill color for the open (hollow) endpoint circles. Defaults to NULL, which uses the active theme's panel background color.

vert_type

Line type for the vertical jump segments. Defaults to "dashed".

show_points

Logical. If FALSE, suppresses all endpoint circles (open and closed). If NULL (the default), circles are shown when there are 50 or fewer points and hidden otherwise.

show_vert

Logical. If FALSE, suppresses the vertical jump segments. If NULL (the default), segments are shown when there are 50 or fewer points and hidden otherwise.

Value

A ggplot2 layer.

Details

Supply either pmf_fun (a PMF such as dbinom, from which the CDF is computed via cumulative summation) or fun (a CDF such as pbinom, from which \(S(x) = 1 - F(x)\) is computed directly).

Examples

  # via PMF
  ggplot() +
    geom_survival_discrete(pmf_fun = dbinom, xlim = c(0, 10), args = list(size = 10, prob = 0.5))


  # via CDF directly
  ggplot() +
    geom_survival_discrete(fun = pbinom, xlim = c(0, 10), args = list(size = 10, prob = 0.5))


  ggplot() +
    geom_survival_discrete(pmf_fun = dpois, xlim = c(0, 15), args = list(lambda = 5))