stat_smooth. ggplot2 0.9.3.1

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 gam for more details.
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

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

Description

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

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.

Aesthetics

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

Examples


c <- ggplot(mtcars, aes(qsec, wt))
c + stat_smooth()

geom_smooth: method="auto" and size of largest group is <1000, so using loess. Use 'method = x' to change the smoothing method.

c + stat_smooth() + geom_point()

geom_smooth: method="auto" and size of largest group is <1000, so using loess. Use 'method = x' to change the smoothing method.


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

geom_smooth: method="auto" and size of largest group is <1000, so using loess. Use 'method = x' to change the smoothing method.


c + stat_smooth(span = 0.9) + geom_point()

geom_smooth: method="auto" and size of largest group is <1000, so using loess. Use 'method = x' to change the smoothing method.

c + stat_smooth(level = 0.99) + geom_point()

geom_smooth: method="auto" and size of largest group is <1000, so using loess. Use 'method = x' to change the smoothing method.

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)

geom_smooth: method="auto" and size of largest group is <1000, so using loess. Use 'method = x' to change the smoothing method.

c + stat_smooth(fill = "blue", size = 2, alpha = 1)

geom_smooth: method="auto" and size of largest group is <1000, so using loess. Use 'method = x' to change the smoothing method.


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

geom_smooth: method="auto" and size of largest group is <1000, so using loess. Use 'method = x' to change the smoothing method.

c + stat_smooth(fill="blue", colour="darkblue", size=2, alpha = 0.2)

geom_smooth: method="auto" and size of largest group is <1000, so using loess. Use 'method = x' to change the smoothing method.

c + geom_point() +
  stat_smooth(fill="blue", colour="darkblue", size=2, alpha = 0.2)

geom_smooth: method="auto" and size of largest group is <1000, so using loess. Use 'method = x' to change the smoothing method.


# 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"))

geom_smooth: method="auto" and size of largest group is <1000, so using loess. Use 'method = x' to change the smoothing method.


# 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))

Add a smoother.