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Plot a Probability Density Function with a Filled Area

Source: R/geom_pdf.R
geom_pdf.Rd

geom_pdf() computes a probability density function and plots it as a filled area. This function is similar to ggplot2::geom_function(), but it shades the area corresponding to a given proportion of the total density.

Usage

geom_pdf(
  mapping = NULL,
  data = NULL,
  stat = StatPDF,
  position = "identity",
  ...,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  fun,
  xlim = NULL,
  n = 101,
  args = list(),
  fill = "grey20",
  color = "black",
  linewidth = NULL,
  alpha = 0.35,
  p = NULL,
  lower.tail = TRUE,
  p_lower = NULL,
  p_upper = NULL,
  shade_outside = FALSE,
  shade_hdr = NULL
)

StatPDF

GeomPDF

Format

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

An object of class GeomPDF (inherits from GeomArea, GeomRibbon, Geom, ggproto, gg) of length 2.

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

Ignored by stat_function(), do not use.

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 arguments passed on to layer()'s params argument. These arguments broadly fall into one of 4 categories below. Notably, further arguments to the position argument, or aesthetics that are required can not be passed through .... Unknown arguments that are not part of the 4 categories below are ignored.

  • Static aesthetics that are not mapped to a scale, but are at a fixed value and apply to the layer as a whole. For example, colour = "red" or linewidth = 3. The geom's documentation has an Aesthetics section that lists the available options. The 'required' aesthetics cannot be passed on to the params. Please note that while passing unmapped aesthetics as vectors is technically possible, the order and required length is not guaranteed to be parallel to the input data.

  • When constructing a layer using a stat_*() function, the ... argument can be used to pass on parameters to the geom part of the layer. An example of this is stat_density(geom = "area", outline.type = "both"). The geom's documentation lists which parameters it can accept.

  • Inversely, when constructing a layer using a geom_*() function, the ... argument can be used to pass on parameters to the stat part of the layer. An example of this is geom_area(stat = "density", adjust = 0.5). The stat's documentation lists which parameters it can accept.

  • The key_glyph argument of layer() may also be passed on through .... This can be one of the functions described as key glyphs, to change the display of the layer in the legend.

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 function to compute the density (e.g. dnorm). The function must accept a numeric vector as its first argument and return density values that integrate (approximately) to 1.

xlim

A numeric vector of length 2 giving the x-range over which to evaluate the PDF.

n

(defaults to 101)Number of points at which to evaluate fun.

args

A named list of additional arguments to pass to fun.

fill

Fill color for the shaded area.

color

Line color for the outline of the density curve.

linewidth

Line width for the outline of the density curve.

alpha

Alpha transparency for the shaded area.

p

(Optional) A numeric value between 0 and 1 specifying the cumulative probability threshold. The area will be shaded up until the point where the cumulative density reaches this value.

lower.tail

Logical; if TRUE (the default) the shaded area extends from the left end of the density up to the threshold. If FALSE, the shading extends from the threshold to the right end.

p_lower

(Optional) A numeric value between 0 and 1 specifying the lower cumulative probability bound. Used with p_upper for two-sided shading.

p_upper

(Optional) A numeric value between 0 and 1 specifying the upper cumulative probability bound. Used with p_lower for two-sided shading.

shade_outside

Logical; if FALSE (the default) shading is applied between p_lower and p_upper. If TRUE, shading is applied to the tails outside that range.

shade_hdr

(Optional) A numeric value between 0 and 1 specifying the coverage of the highest density region (HDR) to shade. The HDR is the smallest region of the domain containing the specified probability mass; for multimodal densities it may be disconnected, producing multiple shaded intervals. Computed following the approach of doi:10.32614/RJ-2023-048 : density values are evaluated on the grid, normalized to sum to 1, sorted in descending order, and cumulated until the target coverage is reached; the density at that threshold determines which regions are shaded. Takes precedence over p, p_lower, and p_upper if specified.

Value

A ggplot2 layer.

Examples

ggplot() +
  geom_pdf(fun = dnorm, xlim = c(-3, 3), p = .975, lower.tail = TRUE)


# Highest density region of a bimodal density
f_bim <- function(x) 0.5 * dnorm(x, -2, 0.5) + 0.5 * dnorm(x, 2, 0.5)
ggplot() +
  geom_pdf(fun = f_bim, xlim = c(-4, 4), shade_hdr = 0.9)