Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Browse files

Re-roxygenize

  • Loading branch information...
commit be4a1a41672106bbf25faadf2369a49a6a42c423 1 parent 0ba6404
@wch wch authored
View
5 NAMESPACE
@@ -235,6 +235,8 @@ S3method(coord_distance,cartesian)
S3method(coord_distance,map)
S3method(coord_distance,polar)
S3method(coord_distance,trans)
+S3method(coord_expand_defaults,default)
+S3method(coord_expand_defaults,polar)
S3method(coord_labels,default)
S3method(coord_labels,flip)
S3method(coord_labels,polar)
@@ -358,6 +360,9 @@ S3method(scale_clone,position_d)
S3method(scale_dimension,continuous)
S3method(scale_dimension,discrete)
S3method(scale_dimension,position_d)
+S3method(scale_expand,default)
+S3method(scale_info,continuous)
+S3method(scale_info,discrete)
S3method(scale_labels,continuous)
S3method(scale_labels,discrete)
S3method(scale_limits,default)
View
2  man/continuous_scale.Rd
@@ -6,7 +6,7 @@
name = NULL, breaks = waiver(),
minor_breaks = waiver(), labels = waiver(),
legend = NULL, limits = NULL, rescaler = rescale,
- oob = censor, expand = c(0, 0), na.value = NA,
+ oob = censor, expand = waiver(), na.value = NA,
trans = "identity", guide = "legend")
}
\arguments{
View
6 man/coord_cartesian.Rd
@@ -2,16 +2,12 @@
\alias{coord_cartesian}
\title{Cartesian coordinates.}
\usage{
- coord_cartesian(xlim = NULL, ylim = NULL, wise = FALSE)
+ coord_cartesian(xlim = NULL, ylim = NULL, wise = NULL)
}
\arguments{
\item{xlim}{limits for the x axis}
\item{ylim}{limits for the y axis}
-
- \item{wise}{If \code{TRUE} will wisely expand the actual
- range of the plot a little, in the way that setting the
- limits on the scales does}
}
\description{
The Cartesian coordinate system is the most familiar, and
View
10 man/coord_expand_defaults.Rd
@@ -0,0 +1,10 @@
+\name{coord_expand_defaults}
+\alias{coord_expand_defaults}
+\title{Set the default expand values for the scale, if NA}
+\usage{
+ coord_expand_defaults(coord, scale, aesthetic = NULL)
+}
+\description{
+ Set the default expand values for the scale, if NA
+}
+
View
6 man/coord_fixed.Rd
@@ -4,7 +4,7 @@
\title{Cartesian coordinates with fixed relationship between x and y scales.}
\usage{
coord_fixed(ratio = 1, xlim = NULL, ylim = NULL,
- wise = FALSE)
+ wise = NULL)
}
\arguments{
\item{ratio}{aspect ratio, expressed as \code{y / x}}
@@ -12,10 +12,6 @@
\item{xlim}{limits for the x axis}
\item{ylim}{limits for the y axis}
-
- \item{wise}{If \code{TRUE} will wisely expand the actual
- range of the plot a little, in the way that setting the
- limits on the scales does}
}
\description{
A fixed scale coordinate system forces a specified ratio
View
6 man/coord_polar.Rd
@@ -2,8 +2,7 @@
\alias{coord_polar}
\title{Polar coordinates.}
\usage{
- coord_polar(theta = "x", start = 0, direction = 1,
- expand = FALSE)
+ coord_polar(theta = "x", start = 0, direction = 1)
}
\arguments{
\item{theta}{variable to map angle to (\code{x} or
@@ -13,9 +12,6 @@
radians}
\item{direction}{1, clockwise; -1, anticlockwise}
-
- \item{expand}{should axes be expanded to slightly outside
- the range of the data? (default: \code{FALSE})}
}
\description{
The polar coordinate system is most commonly used for pie
View
3  man/coord_trans.Rd
@@ -2,7 +2,8 @@
\alias{coord_trans}
\title{Transformed cartesian coordinate system.}
\usage{
- coord_trans(xtrans = "identity", ytrans = "identity")
+ coord_trans(xtrans = "identity", ytrans = "identity",
+ limx = NULL, limy = NULL)
}
\arguments{
\item{ytrans}{transformer for x axis}
View
2  man/discrete_scale.Rd
@@ -4,7 +4,7 @@
\usage{
discrete_scale(aesthetics, scale_name, palette,
name = NULL, breaks = waiver(), labels = waiver(),
- legend = NULL, limits = NULL, expand = c(0, 0),
+ legend = NULL, limits = NULL, expand = waiver(),
na.value = NA, drop = TRUE, guide = "legend")
}
\arguments{
View
4 man/scale_continuous.Rd
@@ -9,9 +9,9 @@
\alias{scale_y_sqrt}
\title{Continuous position scales (x & y).}
\usage{
- scale_x_continuous(..., expand = c(0.05, 0))
+ scale_x_continuous(..., expand = waiver())
- scale_y_continuous(..., expand = c(0.05, 0))
+ scale_y_continuous(..., expand = waiver())
scale_x_log10(...)
View
4 man/scale_date.Rd
@@ -3,10 +3,10 @@
\alias{scale_y_date}
\title{Position scale, date}
\usage{
- scale_x_date(..., expand = c(0.05, 0), breaks = waiver(),
+ scale_x_date(..., expand = waiver(), breaks = waiver(),
minor_breaks = waiver())
- scale_y_date(..., expand = c(0.05, 0), breaks = waiver(),
+ scale_y_date(..., expand = waiver(), breaks = waiver(),
minor_breaks = waiver())
}
\arguments{
View
4 man/scale_datetime.Rd
@@ -3,10 +3,10 @@
\alias{scale_y_datetime}
\title{Position scale, date}
\usage{
- scale_x_datetime(..., expand = c(0.05, 0),
+ scale_x_datetime(..., expand = waiver(),
breaks = waiver(), minor_breaks = waiver())
- scale_y_datetime(..., expand = c(0.05, 0),
+ scale_y_datetime(..., expand = waiver(),
breaks = waiver(), minor_breaks = waiver())
}
\arguments{
View
4 man/scale_discrete.Rd
@@ -3,9 +3,9 @@
\alias{scale_y_discrete}
\title{Discrete position.}
\usage{
- scale_x_discrete(..., expand = c(0, 0.6))
+ scale_x_discrete(..., expand = waiver())
- scale_y_discrete(..., expand = c(0, 0.6))
+ scale_y_discrete(..., expand = waiver())
}
\arguments{
\item{...}{common discrete scale parameters: \code{name},
View
110 man/stat_smooth.Rd
@@ -6,6 +6,11 @@
position = "identity", method = "auto",
formula = y ~ x, se = TRUE, n = 80, fullrange = FALSE,
level = 0.95, na.rm = FALSE, ...)
+
+ 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{
\item{method}{smoothing method (function) to use, eg. lm,
@@ -35,6 +40,33 @@
\item{...}{other arguments are passed to smoothing
function}
+ \item{method}{smoothing method (function) to use, eg. lm,
+ glm, gam, loess, rlm. For datasets with n < 1000 default
+ is \code{\link{loess}}. For datasets with 1000 or more
+ observations defaults to gam, see \code{\link[mgcv]{gam}}
+ for more details.}
+
+ \item{formula}{formula to use in smoothing function, eg.
+ \code{y ~ x}, \code{y ~ poly(x, 2)}, \code{y ~ log(x)}}
+
+ \item{se}{display confidence interval around smooth?
+ (TRUE by default, see level to control}
+
+ \item{fullrange}{should the fit span the full range of
+ the plot, or just the data}
+
+ \item{level}{level of confidence interval to use (0.95 by
+ default)}
+
+ \item{n}{number of points to evaluate smoother at}
+
+ \item{na.rm}{If \code{FALSE} (the default), removes
+ missing values with a warning. If \code{TRUE} silently
+ removes missing values.}
+
+ \item{...}{other arguments are passed to smoothing
+ function}
+
\item{mapping}{The aesthetic mapping, usually constructed
with \code{\link{aes}} or \code{\link{aes_string}}. Only
needs to be set at the layer level if you are overriding
@@ -53,10 +85,18 @@
value} \item{ymin}{lower pointwise confidence interval
around the mean} \item{ymax}{upper pointwise confidence
interval around the mean} \item{se}{standard error}
+
+ a data.frame with additional columns \item{y}{predicted
+ value} \item{ymin}{lower pointwise confidence interval
+ around the mean} \item{ymax}{upper pointwise confidence
+ interval around the mean} \item{se}{standard error}
}
\description{
Aids the eye in seeing patterns in the presence of
overplotting.
+
+ Aids the eye in seeing patterns in the presence of
+ overplotting.
}
\details{
Calculation is performed by the (currently undocumented)
@@ -67,6 +107,15 @@
\code{glm} where the normal confidence interval is
constructed on the link scale, and then back-transformed
to the response scale.
+
+ Calculation is performed by the (currently undocumented)
+ \code{predictdf} generic function and its methods. For
+ most methods the confidence bounds are computed using the
+ \code{\link{predict}} method - the exceptions are
+ \code{loess} which uses a t-based approximation, and for
+ \code{glm} where the normal confidence interval is
+ constructed on the link scale, and then back-transformed
+ to the response scale.
}
\examples{
\donttest{
@@ -126,10 +175,71 @@ qplot(Age, as.numeric(Kyphosis) - 1, data = kyphosis) +
qplot(Age, as.numeric(Kyphosis) - 1, data=kyphosis) +
stat_smooth(method="glm", family="binomial", formula = y ~ ns(x, 2))
}
+\donttest{
+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))
+}
}
\seealso{
\code{\link{lm}} for linear smooths, \code{\link{glm}}
for generalised linear smooths, \code{\link{loess}} for
local smooths
+
+ \code{\link{lm}} for linear smooths, \code{\link{glm}}
+ for generalised linear smooths, \code{\link{loess}} for
+ local smooths
}
Please sign in to comment.
Something went wrong with that request. Please try again.