Removed xxx.r (build_accessor file) and @name tags, added functions t…

…o geoms/positions/stats

DESCRIPTION

@@ -156,5 +156,4 @@ Collate:
     'utilities.r'
     'xxx-codegen.r'
     'xxx-digest.r'
-    'xxx.r'
     'zxx.r'

R/geom-abline.r

@@ -10,8 +10,7 @@
 #' (\code{geom_abline(intercept=0, slope=1)}) then the line will be the same
 #' in all panels.  If the intercept and slope are stored in the data, then 
 #' they can vary from panel to panel.  See the examples for more ideas.
-#' 
-#' @name geom_abline
+#'
 #' @seealso \code{\link{stat_smooth}} to add lines derived from the data,
 #'  \code{\link{geom_hline}} for horizontal lines,
 #'  \code{\link{geom_vline}} for vertical lines
@@ -49,6 +48,10 @@
 #' # It's actually a bit easier to do this with stat_smooth
 #' p + geom_smooth(aes(group=cyl), method="lm")
 #' p + geom_smooth(aes(group=cyl), method="lm", fullrange=TRUE)
+geom_abline <- function (mapping = NULL, data = NULL, stat = "abline", position = "identity", ...) { 
+  GeomAbline$new(mapping = mapping, data = data, stat = stat, position = position, ...)
+}
+
 GeomAbline <- proto(Geom, {
   objname <- "abline"
 

R/geom-bar-.r

@@ -28,8 +28,7 @@
 #' Naomi Robbins has a nice
 #' \href{http://www.b-eye-network.com/view/index.php?cid=2468}{article on this topic}.  
 #' This is the reason it doesn't make sense to use a log-scaled y axis with a bar chart
-#' 
-#' @name geom_bar
+#'
 #' @seealso \code{\link{stat_bin}} for more details of the binning alogirithm, 
 #'   \code{\link{position_dodge}} for creating side-by-side barcharts, 
 #'   \code{\link{position_stack}} for more info on stacking,
@@ -103,6 +102,10 @@
 #' "suv", "compact", "2seater", "subcompact", "pickup"))
 #' m <- ggplot(mpg, aes(manufacturer, fill=class))
 #' m + geom_bar()
+geom_bar <- function (mapping = NULL, data = NULL, stat = "bin", position = "stack", ...) {
+  GeomBar$new(mapping = mapping, data = data, stat = stat, position = position, ...)
+}
+
 GeomBar <- proto(Geom, {
   objname <- "bar"
 

R/geom-bar-histogram.r

@@ -9,7 +9,6 @@
 #' may need to look at a few to uncover the full story behind your data.
 #'
 #'
-#' @name geom_histogram
 #' @export 
 #' @examples
 #' # Simple examples
@@ -104,6 +103,10 @@
 #' # Which looks better when the distributions are more distinct
 #' ggplot(diamonds, aes(depth, fill = cut)) +
 #'   geom_density(alpha = 0.2) + xlim(55, 70)
+geom_histogram <- function (mapping = NULL, data = NULL, stat = "bin", position = "stack", ...) { 
+  GeomHistogram$new(mapping = mapping, data = data, stat = stat, position = position, ...)
+}
+
 GeomHistogram <- proto(GeomBar, {
   objname <- "histogram"
 

R/geom-bin2d.r

@@ -1,13 +1,16 @@
 #' Add heatmap of 2d bin counts.
-#' 
-#' @name geom_bin2d
+#'
 #' @export
 #' @examples
 #' d <- ggplot(diamonds, aes(x = x, y = y)) + xlim(4,10) + ylim(4,10)
 #' d + geom_bin2d()
 #' d + geom_bin2d(binwidth = c(0.1, 0.1))
 #'
 #' # See ?stat_bin2d for more examples  
+geom_bin2d <- function (mapping = NULL, data = NULL, stat = "bin2d", position = "identity", ...) { 
+  GeomBin2d$new(mapping = mapping, data = data, stat = stat, position = position, ...)
+}
+
 GeomBin2d <- proto(Geom, {
   draw <- function(., data, scales, coordinates, ...) {
     GeomRect$draw(data, scales, coordinates, ...)

R/geom-blank.r

@@ -3,11 +3,14 @@
 #' The blank geom draws nothing, but can be a useful way of ensuring common
 #' scales between different plots.
 #'
-#' @name geom_blank
 #' @export
 #' @examples
 #' qplot(length, rating, data=movies, geom="blank")
 #' # Nothing to see here!
+geom_blank <- function (mapping = NULL, data = NULL, stat = "identity", position = "identity", ...) { 
+  GeomBlank$new(mapping = mapping, data = data, stat = stat, position = position, ...)
+}
+
 GeomBlank <- proto(Geom, {
   objname <- "blank"
 

R/geom-boxplot.r

@@ -1,6 +1,5 @@
 #' Box and whiskers plot.
 #'
-#' @name geom_boxplot
 #' @seealso \code{\link{stat_quantile}} to view quantiles conditioned on a
 #'   continuous variable,  \code{\link{geom_jitter}} for another way to look 
 #'   at conditional distributions"
@@ -58,6 +57,13 @@
 #' b + geom_boxplot(stat = "identity")
 #' b + geom_boxplot(stat = "identity") + coord_flip()
 #' b + geom_boxplot(aes(fill = X1), stat = "identity")
+geom_boxplot <- function (mapping = NULL, data = NULL, stat = "boxplot", position = "dodge", 
+outlier.colour = "black", outlier.shape = 16, outlier.size = 2, ...) {
+  GeomBoxplot$new(mapping = mapping, data = data, stat = stat, 
+  position = position, outlier.colour = outlier.colour, outlier.shape = outlier.shape, 
+  outlier.size = outlier.size, ...)
+}
+
 GeomBoxplot <- proto(Geom, {
   objname <- "boxplot"
 

R/geom-crossbar.r

@@ -1,6 +1,5 @@
 #' Hollow bar with middle indicated by horizontal line.
-#' 
-#' @name geom_crossbar
+#'
 #' @param fatten a multiplicate factor to fatten middle bar by
 #' @seealso \code{\link{geom_errorbar}} for error bars,
 #' \code{\link{geom_pointrange}} and \code{\link{geom_linerange}} for other
@@ -9,6 +8,12 @@
 #' @export
 #' @examples
 #' # See geom_linerange for examples
+geom_crossbar <- function (mapping = NULL, data = NULL, stat = "identity", position = "identity", 
+fatten = 2, ...) { 
+  GeomCrossbar$new(mapping = mapping, data = data, stat = stat, 
+  position = position, fatten = fatten, ...)
+}
+
 GeomCrossbar <- proto(Geom, {
   objname <- "crossbar"
 

R/geom-error.r

@@ -1,6 +1,5 @@
 #' Error bars.
-#' 
-#' @name geom_errorbar
+#'
 #' @seealso \code{\link{geom_pointrange}}: range indicated by straight line,
 #'   with point in the middle; \code{\link{geom_linerange}}: range indicated
 #'   by straight line; \code{\link{geom_crossbar}}: hollow bar with middle
@@ -41,6 +40,10 @@
 #' # groups which define the lines - here the groups in the 
 #' # original dataframe
 #' p + geom_line(aes(group=group)) + geom_errorbar(limits, width=0.2)    
+geom_errorbar <- function (mapping = NULL, data = NULL, stat = "identity", position = "identity", ...) { 
+  GeomErrorbar$new(mapping = mapping, data = data, stat = stat, position = position, ...)
+}
+
 GeomErrorbar <- proto(Geom, {
   objname <- "errorbar"
 

R/geom-errorh.r

@@ -1,6 +1,5 @@
 #' Horizontal error bars
-#' 
-#' @name geom_errorbarh
+#'
 #' @seealso \code{\link{geom_errorbar}}: vertical error bars
 #' @param height height of errorbars
 #' @export
@@ -19,6 +18,10 @@
 #'   geom_errorbarh(aes(xmax = resp + se, xmin = resp - se))
 #' p + geom_point() +
 #'   geom_errorbarh(aes(xmax = resp + se, xmin = resp - se, height = .2))
+geom_errorbarh <- function (mapping = NULL, data = NULL, stat = "identity", position = "identity", ...) { 
+  GeomErrorbarh$new(mapping = mapping, data = data, stat = stat, position = position, ...)
+}
+
 GeomErrorbarh <- proto(Geom, {
   objname <- "errorbarh"
 

R/geom-freqpoly.r

@@ -1,18 +1,21 @@
 #' Frequency polygon.
 #'
-#' @name geom_freqpoly
 #' @seealso \code{\link{geom_histogram}}: histograms
 #' @export
 #' @examples
-#' qplot(carat, data = diamonds, geom="freqpoly")
-#' qplot(carat, data = diamonds, geom="freqpoly", binwidth = 0.1)
-#' qplot(carat, data = diamonds, geom="freqpoly", binwidth = 0.01)
+#' qplot(carat, data = diamonds, geom = "freqpoly")
+#' qplot(carat, data = diamonds, geom = "freqpoly", binwidth = 0.1)
+#' qplot(carat, data = diamonds, geom = "freqpoly", binwidth = 0.01)
 #' 
-#' qplot(price, data = diamonds, geom="freqpoly", binwidth = 1000)
-#' qplot(price, data = diamonds, geom="freqpoly", binwidth = 1000, 
+#' qplot(price, data = diamonds, geom = "freqpoly", binwidth = 1000)
+#' qplot(price, data = diamonds, geom = "freqpoly", binwidth = 1000, 
 #'   colour = color)
-#' qplot(price, ..density.., data = diamonds, geom="freqpoly", 
+#' qplot(price, ..density.., data = diamonds, geom = "freqpoly", 
 #'   binwidth = 1000, colour = color)
+geom_freqpoly <- function (mapping = NULL, data = NULL, stat = "bin", position = "identity", ...) { 
+  GeomFreqpoly$new(mapping = mapping, data = data, stat = stat, position = position, ...)
+}
+
 GeomFreqpoly <- proto(Geom, {
   objname <- "freqpoly"
 

R/geom-hex.r

@@ -1,9 +1,12 @@
 #' Hexagon bining.
-#' 
-#' @name geom_hex
+#'
 #' @export
 #' @examples
 #' # See ?stat_binhex for examples  
+geom_hex <- function (mapping = NULL, data = NULL, stat = "binhex", position = "identity", ...) { 
+  GeomHex$new(mapping = mapping, data = data, stat = stat, position = position, ...)
+}
+
 GeomHex <- proto(Geom, {
   objname <- "hex"
 

R/geom-hline.r

@@ -10,7 +10,6 @@
 #' intercept for each panel using a data.frame. See the examples for the
 #' differences
 #'
-#' @name geom_hline
 #' @seealso \code{\link{geom_vline}} for vertical lines, 
 #'  \code{\link{geom_abline}} for lines defined by a slope and intercept,
 #'  \code{\link{geom_segment}} for a more general approach
@@ -28,6 +27,10 @@
 #' 
 #' hline.data <- data.frame(z = 1:4, vs = c(0,0,1,1), am = c(0,1,0,1))
 #' p + geom_hline(aes(yintercept = z), hline.data)
+geom_hline <- function (mapping = NULL, data = NULL, stat = "hline", position = "identity", ...) { 
+  GeomHline$new(mapping = mapping, data = data, stat = stat, position = position, ...)
+}
+
 GeomHline <- proto(Geom, {
   objname <- "hline"
 

R/geom-linerange.r

@@ -1,6 +1,5 @@
 #' An interval represented by a vertical line.
 #'
-#' @name geom_linerange
 #' @seealso \code{\link{geom_errorbar}}: error bars;
 #'   \code{\link{geom_pointrange}}: range indicated by straight line, with
 #'   point in the middle; \code{\link{geom_crossbar}}: hollow bar with middle
@@ -28,6 +27,10 @@
 #' 
 #' # Use coord_flip to flip the x and y axes
 #' se + geom_linerange() + coord_flip()
+geom_linerange <- function (mapping = NULL, data = NULL, stat = "identity", position = "identity", ...) { 
+  GeomLinerange$new(mapping = mapping, data = data, stat = stat, position = position, ...)
+}
+
 GeomLinerange <- proto(Geom, {
   objname <- "linerange"
 

R/geom-path-.r

@@ -1,6 +1,5 @@
 #' Connect observations in original order
 #' 
-#' @name geom_path
 #' @param lineend Line end style (round, butt, square)
 #' @param linejoin Line join style (round, mitre, bevel)
 #' @param linemitre Line mitre limit (number greater than 1)
@@ -87,6 +86,12 @@
 #' # Arrow defaults to "last"
 #' c + geom_path(arrow = arrow())
 #' c + geom_path(arrow = arrow(angle = 15, ends = "both", length = unit(0.6, "inches")))
+geom_path <- function (mapping = NULL, data = NULL, stat = "identity", position = "identity", 
+lineend = "butt", linejoin = "round", linemitre = 1, na.rm = FALSE, ...) { 
+  GeomPath$new(mapping = mapping, data = data, stat = stat, position = position, 
+  lineend = lineend, linejoin = linejoin, linemitre = linemitre, na.rm = na.rm, ...)
+}
+
 GeomPath <- proto(Geom, {
   objname <- "path"
 

R/geom-path-contour.r

@@ -1,10 +1,15 @@
 #' Display contours of a 3d surface in 2d.
 #'
-#' @name geom_contour
 #' @seealso \code{\link{geom_density2d}}: 2d density contours
 #' @export
 #' @examples
 #' # See stat_contour for examples
+geom_contour <- function (mapping = NULL, data = NULL, stat = "contour", position = "identity", 
+lineend = "butt", linejoin = "round", linemitre = 1, na.rm = FALSE, ...) { 
+  GeomContour$new(mapping = mapping, data = data, stat = stat, position = position,
+  lineend = lineend, linejoin = linejoin, linemitre = linemitre, na.rm = na.rm, ...)
+}
+
 GeomContour <- proto(GeomPath, {
   objname <- "contour"
 

R/geom-path-density2d.r

@@ -4,13 +4,18 @@
 #' results with contours.
 #' 
 #' This can be useful for dealing with overplotting.
-#' 
-#' @name geom_density2d
+#'
 #' @seealso \code{\link{geom_contour}} for contour drawing geom, 
 #'  \code{\link{stat_sum}} for another way of dealing with overplotting
 #' @export
 #' @examples
 #' # See stat_density2d for examples
+geom_density2d <- function (mapping = NULL, data = NULL, stat = "density2d", position = "identity", 
+lineend = "butt", linejoin = "round", linemitre = 1, na.rm = FALSE, ...) { 
+  GeomDensity2d$new(mapping = mapping, data = data, stat = stat, position = position, 
+  lineend = lineend, linejoin = linejoin, linemitre = linemitre, na.rm = na.rm, ...)
+}
+
 GeomDensity2d <- proto(GeomPath, {
   objname <- "density2d"
 

R/geom-path-line.r

@@ -1,6 +1,5 @@
 #' Connect observations, ordered by x value.
 #'
-#' @name geom_line
 #' @seealso \code{\link{geom_path}}: connect observations in data order, 
 #'  \code{\link{geom_segment}}: draw line segments,
 #'  \code{\link{geom_ribbon}}: fill between line and x-axis
@@ -56,6 +55,10 @@
 #' dfm <- melt(df, id.var = c("id", "group"))
 #' ggplot(dfm, aes(variable, value, group = id, colour = group)) + 
 #'   geom_path(alpha = 0.5)
+geom_line <- function (mapping = NULL, data = NULL, stat = "identity", position = "identity", ...) { 
+  GeomLine$new(mapping = mapping, data = data, stat = stat, position = position, ...)
+}
+
 GeomLine <- proto(GeomPath, {
   objname <- "line"
 

R/geom-path-step.r

@@ -1,6 +1,5 @@
 #' Connect observations by stairs.
 #'
-#' @name geom_step
 #' @param direction direction of stairs: 'vh' for vertical then horizontal, or
 #'   'hv' for horizontal then vertical
 #' @export
@@ -22,6 +21,12 @@
 #'   trt = sample(c("a", "b"), 50, rep = T)
 #' )
 #' qplot(seq_along(x), x, data = df, geom="step", colour = trt)
+geom_step <- function (mapping = NULL, data = NULL, stat = "identity", position = "identity", 
+direction = "hv", ...) {
+  GeomStep$new(mapping = mapping, data = data, stat = stat, position = position, 
+  direction = direction, ...)
+}
+
 GeomStep <- proto(Geom, {
   objname <- "step"
 

R/geom-point-jitter.r

@@ -4,7 +4,6 @@
 #' 'jitter'.  See \code{\link{position_jitter}} to see how to adjust amount 
 #' of jittering.
 #' 
-#' @name geom_jitter
 #' @seealso
 #'  \code{\link{geom_point}} for regular, unjittered points, 
 #'  \code{\link{geom_boxplot}} for another way of looking at the conditional
@@ -28,6 +27,12 @@
 #' qplot(mpaa, rating, data=movies, geom="jitter")
 #' qplot(mpaa, rating, data=movies, geom=c("boxplot","jitter"))
 #' qplot(mpaa, rating, data=movies, geom=c("jitter", "boxplot"))
+geom_jitter <- function (mapping = NULL, data = NULL, stat = "identity", position = "jitter", 
+na.rm = FALSE, ...) { 
+  GeomJitter$new(mapping = mapping, data = data, stat = stat, position = position, 
+  na.rm = na.rm, ...)
+}
+
 GeomJitter <- proto(GeomPoint, {
   objname <- "jitter"
 

R/geom-pointrange.r

@@ -1,6 +1,5 @@
 #' An interval represented by a vertical line, with a point in the middle.
 #' 
-#' @name geom_pointrange
 #' @seealso
 #'  \code{\link{geom_errorbar}} for error bars,
 #'  \code{\link{geom_linerange}} for range indicated by straight line, + examples,
@@ -10,6 +9,10 @@
 #' @export
 #' @examples
 #' # See geom_linerange for examples
+geom_pointrange <- function (mapping = NULL, data = NULL, stat = "identity", position = "identity", ...) { 
+  GeomPointrange$new(mapping = mapping, data = data, stat = stat, position = position, ...)
+}
+
 GeomPointrange <- proto(Geom, {
   objname <- "pointrange"