stat_smooth

0th

Percentile

Add a smoother.

Aids the eye in seeing patterns in the presence of overplotting.

Usage
stat_smooth(mapping = NULL, data = NULL, geom = "smooth",
    position = "identity", method = "auto",
    formula = y ~ x, se = TRUE, n = 80, fullrange = FALSE,
    level = 0.95, na.rm = FALSE, ...)
Arguments
method
smoothing method (function) to use, eg. lm, glm, gam, loess, rlm. For datasets with n < 1000 default is loess. For datasets with 1000 or more observations defaults to gam, see
formula
formula to use in smoothing function, eg. y ~ x, y ~ poly(x, 2), y ~ log(x)
se
display confidence interval around smooth? (TRUE by default, see level to control
fullrange
should the fit span the full range of the plot, or just the data
level
level of confidence interval to use (0.95 by default)
n
number of points to evaluate smoother at
na.rm
If FALSE (the default), removes missing values with a warning. If TRUE silently removes missing values.
...
other arguments are passed to smoothing function
mapping
The aesthetic mapping, usually constructed with aes or aes_string. Only needs to be set at the layer level if you are overriding the plot defaults.
data
A layer specific dataset - only needed if you want to override the plot defaults.
geom
The geometric object to use display the data
position
The position adjustment to use for overlappling points on this layer
Details

Calculation is performed by the (currently undocumented) predictdf generic function and its methods. For most methods the confidence bounds are computed using the predict method - the exceptions are loess which uses a t-based approximation, and for glm where the normal confidence interval is constructed on the link scale, and then back-transformed to the response scale.

Value

  • a data.frame with additional columns
  • ypredicted value
  • yminlower pointwise confidence interval around the mean
  • ymaxupper pointwise confidence interval around the mean
  • sestandard error

Aesthetics

[results=rd,stage=build]{ggplot2:::rd_aesthetics("stat", "smooth")} c <- ggplot(mtcars, aes(qsec, wt)) c + stat_smooth() c + stat_smooth() + geom_point()

# Adjust parameters c + stat_smooth(se = FALSE) + geom_point()

c + stat_smooth(span = 0.9) + geom_point() c + stat_smooth(level = 0.99) + geom_point() c + stat_smooth(method = "lm") + geom_point()

library(splines) library(MASS) c + stat_smooth(method = "lm", formula = y ~ ns(x,3)) + geom_point() c + stat_smooth(method = rlm, formula= y ~ ns(x,3)) + geom_point()

# The default confidence band uses a transparent colour. # This currently only works on a limited number of graphics devices # (including Quartz, PDF, and Cairo) so you may need to set the # fill colour to a opaque colour, as shown below c + stat_smooth(fill = "grey50", size = 2, alpha = 1) c + stat_smooth(fill = "blue", size = 2, alpha = 1)

# The colour of the line can be controlled with the colour aesthetic c + stat_smooth(fill="blue", colour="darkblue", size=2) c + stat_smooth(fill="blue", colour="darkblue", size=2, alpha = 0.2) c + geom_point() + stat_smooth(fill="blue", colour="darkblue", size=2, alpha = 0.2)

# Smoothers for subsets c <- ggplot(mtcars, aes(y=wt, x=mpg)) + facet_grid(. ~ cyl) c + stat_smooth(method=lm) + geom_point() c + stat_smooth(method=lm, fullrange = TRUE) + geom_point()

# Geoms and stats are automatically split by aesthetics that are factors c <- ggplot(mtcars, aes(y=wt, x=mpg, colour=factor(cyl))) c + stat_smooth(method=lm) + geom_point() c + stat_smooth(method=lm, aes(fill = factor(cyl))) + geom_point() c + stat_smooth(method=lm, fullrange=TRUE, alpha = 0.1) + geom_point()

# Use qplot instead qplot(qsec, wt, data=mtcars, geom=c("smooth", "point"))

# Example with logistic regression data("kyphosis", package="rpart") qplot(Age, Kyphosis, data=kyphosis) qplot(Age, data=kyphosis, facets = . ~ Kyphosis, binwidth = 10) qplot(Age, Kyphosis, data=kyphosis, position="jitter") qplot(Age, Kyphosis, data=kyphosis, position=position_jitter(height=0.1))

qplot(Age, as.numeric(Kyphosis) - 1, data = kyphosis) + stat_smooth(method="glm", family="binomial") qplot(Age, as.numeric(Kyphosis) - 1, data=kyphosis) + stat_smooth(method="glm", family="binomial", formula = y ~ ns(x, 2))

lm for linear smooths, glm for generalised linear smooths, loess for local smooths

Aliases
  • stat_smooth
Documentation reproduced from package ggplot2, version 0.9.3.1, License: GPL-2

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