Re-roxygenize

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)

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{

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

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
+}
+

man/coord_fixed.Rd

@@ -4,18 +4,14 @@
 \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}}
 
   \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

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

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}

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{

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(...)
 

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{

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{

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},

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{
@@ -121,6 +170,63 @@ 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))
+}
+\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) +
@@ -131,5 +237,9 @@ qplot(Age, as.numeric(Kyphosis) - 1, data=kyphosis) +
   \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
 }