Fix documentation cross-refs.

Includes exporting and documenting layer and waiver
tidyverse · Dec 20, 2011 · 08461b8 · 08461b8
1 parent f47bffa
commit 08461b8
Show file tree

Hide file tree

Showing 21 changed files with 82 additions and 37 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -81,6 +81,7 @@ export(label_parsed)
 export(label_value)
 export(labs)
 export(last_plot)
+export(layer)
 export(map_data)
 export(mean_cl_boot)
 export(mean_cl_normal)
@@ -194,6 +195,7 @@ export(theme_text)
 export(theme_update)
 export(update_element)
 export(update_labels)
+export(waiver)
 export(xlab)
 export(xlim)
 export(ylab)

diff --git a/R/coord-map.r b/R/coord-map.r
@@ -7,9 +7,10 @@
 #' a better (or more correct) way to do this, please let me know
 #' 
 #' @export
-#' @param projection projection to use, see \code{\link{mapproject}} for
-#'   list
-#' @param ... other arguments passed on to \code{\link{mapproject}}
+#' @param projection projection to use, see
+#'    \code{\link[mapproj]{mapproject}} for list
+#' @param ... other arguments passed on to
+#'   \code{\link[mapproj]{mapproject}}
 #' @param orientation projection orientation, which defaults to 
 #'  \code{c(90, 0, mean(range(x)))}.  This is not optimal for many
 #'  projections, so you will have to supply your own.

diff --git a/R/fortify-map.r b/R/fortify-map.r
@@ -5,7 +5,7 @@
 #' 
 #' @method fortify map
 #' @S3method fortify map
-#' @seealso \code{\link{map_data}} and \code{\link{border}}
+#' @seealso \code{\link{map_data}} and \code{\link{borders}}
 #' @param model map object
 #' @param data not used by this method
 #' @param ... not used by this method
@@ -34,13 +34,14 @@ fortify.map <- function(model, data, ...) {
 
 #' Create a data frame of map data.
 #' 
-#' @param map name of map provided by \code{\link{maps}} package.  These 
-#'   include \code{\link{county}}, \code{\link{france}}, \code{\link{italy}},
-#'   \code{\link{nz}}, \code{\link{state}}, \code{\link{usa}}, 
-#'   \code{\link{world}}, \code{\link{world2}}.
+#' @param map name of map provided by the \pkg{maps} package.  These 
+#'   include \code{\link[maps]{county}}, \code{\link[maps]{france}},
+#'   \code{\link[maps]{italy}}, \code{\link[maps]{nz}}, 
+#'   \code{\link[maps]{state}}, \code{\link[maps]{usa}}, 
+#'   \code{\link[maps]{world}}, \code{\link[maps]{world2}}.
 #' @param region name of subregions to include.  Defaults to \code{.} which
-#'   includes all subregion.  See documentation for \code{\link{map}} for
-#'   more details.
+#'   includes all subregion.  See documentation for \code{\link[maps]{map}}
+#'   for more details.
 #' @param exact should the \code{region} be treated as a regular expression
 #'   (\code{FALSE}) or as a fixed string (\code{TRUE}).
 #' @param ... all other arguments passed on to \code{\link[maps]{map}}

diff --git a/R/fortify-multcomp.r b/R/fortify-multcomp.r
@@ -1,7 +1,7 @@
 #' Fortify methods for objects produced by \pkg{multcomp}
 #'
 #' @param model an object of class \code{glht}, \code{confint.glht},
-#'  \code{summary.glht} or \code{\link{cld}}
+#'  \code{summary.glht} or \code{\link[multcomp]{cld}}
 #' @param data,... other arguments to the generic ignored in this method.
 #' @name fortify-multcomp
 #' @examples

diff --git a/R/guide-colorbar.r b/R/guide-colorbar.r
@@ -10,7 +10,7 @@
 ##'
 ##' @name guide_colorbar
 ##' @title Colorbar guide
-##' @param title A character string or expression indicating a title of guide. If \code{NULL}, the title is not shown. By default (\code{\link{waiver()}}), the name of the scale object or tha name specified in \code{\link{labs}} is used for the title.
+##' @param title A character string or expression indicating a title of guide. If \code{NULL}, the title is not shown. By default (\code{\link{waiver}}), the name of the scale object or tha name specified in \code{\link{labs}} is used for the title.
 ##' @param title.position A character string indicating the position of a title. One of "top" (default for a vertical guide), "bottom", "left" (default for a horizontal guide), or "right."
 ##' @param title.theme A theme object for rendering the title text. Usually the object of \code{\link{theme_text}} is expected. By default, the theme is specified by \code{legend.title} in \code{\link{opts}} or theme.
 ##' @param title.hjust A numeric specifying horizontal justification of the title text.

diff --git a/R/guide-legend.r b/R/guide-legend.r
@@ -9,7 +9,7 @@
 ##' 
 ##' @name guide_legend
 ##' @title Legend guide
-##' @param title A character string or expression indicating a title of guide. If \code{NULL}, the title is not shown. By default (\code{\link{waiver()}}), the name of the scale object or tha name specified in \code{\link{labs}} is used for the title.
+##' @param title A character string or expression indicating a title of guide. If \code{NULL}, the title is not shown. By default (\code{\link{waiver}}), the name of the scale object or tha name specified in \code{\link{labs}} is used for the title.
 ##' @param title.position A character string indicating the position of a title. One of "top" (default for a vertical guide), "bottom", "left" (default for a horizontal guide), or "right."
 ##' @param title.theme A theme object for rendering the title text. Usually the object of \code{\link{theme_text}} is expected. By default, the theme is specified by \code{legend.title} in \code{\link{opts}} or theme.
 ##' @param title.hjust A numeric specifying horizontal justification of the title text.

diff --git a/R/layer.r b/R/layer.r
@@ -231,6 +231,10 @@ Layer <- proto(expr = {
   class <- function(.) "layer"
 })
 
+#' Create a new layer
+#' 
+#' @keywords internal
+#' @export
 layer <- Layer$new
 
 # Determine if aesthetic is calculated

diff --git a/R/plot-construction.r b/R/plot-construction.r
@@ -15,7 +15,7 @@
 #'
 #' @param p plot object
 #' @param object component to add
-#' @seealso \code{\link{set_last_plot}}, \code{\link{ggplot}}
+#' @seealso \code{\link{ggplot}}
 #' @method + ggplot
 #' @S3method "+" ggplot
 #' @rdname ggplot-add

diff --git a/R/plot-render.r b/R/plot-render.r
@@ -151,7 +151,7 @@ ggplot_gtable <- function(data) {
 #' @param x plot to display
 #' @param newpage draw new (empty) page first?
 #' @param vp viewport to draw plot in
-#' @param ... other arguments passed on to \code{\link{ggplotGrob}}
+#' @param ... other arguments not used by this method
 #' @keywords hplot
 #' @S3method print ggplot
 #' @method print ggplot

diff --git a/R/utilities.r b/R/utilities.r
@@ -165,8 +165,17 @@ should_stop <- function(expr) {
 }
 
 
-# Waive decision
+#' A waiver object.
+#' 
+#' A waiver is a "flag" object, similar to \code{NULL}, that indicates the 
+#' calling function should just use the default value.  It is used in certain
+#' functions to distinguish between displaying nothing (\code{NULL}) and
+#' displaying a default value calculated elsewhere (\code{waiver()})
+#' 
+#' @export
+#' @keywords internal
 waiver <- function() structure(NULL, class="waiver")
+
 is.waive <- function(x) inherits(x, "waiver")
 
 

diff --git a/man/borders.Rd b/man/borders.Rd
@@ -22,8 +22,7 @@
   Create a layer of map borders.
 }
 \examples{
-require("maps")
-require("ggplot2")
+if (require("maps")) {
 
 ia <- map_data("county", "iowa")
 mid_range <- function(x) mean(range(x))
@@ -38,5 +37,7 @@ ggplot(capitals, aes(long, lat)) +
   borders("state") +
   geom_point(aes(size = pop)) +
   scale_area()
+
+}
 }
 
diff --git a/man/coord_map.Rd b/man/coord_map.Rd
@@ -7,10 +7,10 @@
 }
 \arguments{
   \item{projection}{projection to use, see
-  \code{\link{mapproject}} for list}
+  \code{\link[mapproj]{mapproject}} for list}
 
   \item{...}{other arguments passed on to
-  \code{\link{mapproject}}}
+  \code{\link[mapproj]{mapproject}}}
 
   \item{orientation}{projection orientation, which defaults
   to \code{c(90, 0, mean(range(x)))}.  This is not optimal

diff --git a/man/fortify-multcomp.Rd b/man/fortify-multcomp.Rd
@@ -17,7 +17,7 @@
 \arguments{
   \item{model}{an object of class \code{glht},
   \code{confint.glht}, \code{summary.glht} or
-  \code{\link{cld}}}
+  \code{\link[multcomp]{cld}}}
 
   \item{data,...}{other arguments to the generic ignored in
   this method.}

diff --git a/man/fortify.map.Rd b/man/fortify.map.Rd
@@ -28,6 +28,6 @@ qplot(long, lat, data = tx, geom = "polygon", group = group,
 }
 }
 \seealso{
-  \code{\link{map_data}} and \code{\link{border}}
+  \code{\link{map_data}} and \code{\link{borders}}
 }
 
diff --git a/man/ggplot-add.Rd b/man/ggplot-add.Rd
@@ -25,6 +25,6 @@
   override current coordinate faceting }
 }
 \seealso{
-  \code{\link{set_last_plot}}, \code{\link{ggplot}}
+  \code{\link{ggplot}}
 }
 
diff --git a/man/guide_colorbar.Rd b/man/guide_colorbar.Rd
@@ -15,9 +15,9 @@
 \arguments{
   \item{title}{A character string or expression indicating
   a title of guide. If \code{NULL}, the title is not shown.
-  By default (\code{\link{waiver()}}), the name of the
-  scale object or tha name specified in \code{\link{labs}}
-  is used for the title.}
+  By default (\code{\link{waiver}}), the name of the scale
+  object or tha name specified in \code{\link{labs}} is
+  used for the title.}
 
   \item{title.position}{A character string indicating the
   position of a title. One of "top" (default for a vertical

diff --git a/man/guide_legend.Rd b/man/guide_legend.Rd
@@ -15,9 +15,9 @@
 \arguments{
   \item{title}{A character string or expression indicating
   a title of guide. If \code{NULL}, the title is not shown.
-  By default (\code{\link{waiver()}}), the name of the
-  scale object or tha name specified in \code{\link{labs}}
-  is used for the title.}
+  By default (\code{\link{waiver}}), the name of the scale
+  object or tha name specified in \code{\link{labs}} is
+  used for the title.}
 
   \item{title.position}{A character string indicating the
   position of a title. One of "top" (default for a vertical

diff --git a/man/layer.Rd b/man/layer.Rd
@@ -0,0 +1,11 @@
+\name{layer}
+\alias{layer}
+\title{Create a new layer}
+\usage{
+  layer(...)
+}
+\description{
+  Create a new layer
+}
+\keyword{internal}
+
diff --git a/man/map_data.Rd b/man/map_data.Rd
@@ -5,15 +5,16 @@
   map_data(map, region = ".", exact = FALSE, ...)
 }
 \arguments{
-  \item{map}{name of map provided by \code{\link{maps}}
-  package.  These include \code{\link{county}},
-  \code{\link{france}}, \code{\link{italy}},
-  \code{\link{nz}}, \code{\link{state}}, \code{\link{usa}},
-  \code{\link{world}}, \code{\link{world2}}.}
+  \item{map}{name of map provided by the \pkg{maps}
+  package.  These include \code{\link[maps]{county}},
+  \code{\link[maps]{france}}, \code{\link[maps]{italy}},
+  \code{\link[maps]{nz}}, \code{\link[maps]{state}},
+  \code{\link[maps]{usa}}, \code{\link[maps]{world}},
+  \code{\link[maps]{world2}}.}
 
   \item{region}{name of subregions to include.  Defaults to
   \code{.} which includes all subregion.  See documentation
-  for \code{\link{map}} for more details.}
+  for \code{\link[maps]{map}} for more details.}
 
   \item{exact}{should the \code{region} be treated as a
   regular expression (\code{FALSE}) or as a fixed string

diff --git a/man/print.ggplot.Rd b/man/print.ggplot.Rd
@@ -12,8 +12,7 @@
 
   \item{vp}{viewport to draw plot in}
 
-  \item{...}{other arguments passed on to
-  \code{\link{ggplotGrob}}}
+  \item{...}{other arguments not used by this method}
 }
 \description{
   Draw plot on current graphics device.

diff --git a/man/waiver.Rd b/man/waiver.Rd
@@ -0,0 +1,16 @@
+\name{waiver}
+\alias{waiver}
+\title{A waiver object.}
+\usage{
+  waiver()
+}
+\description{
+  A waiver is a "flag" object, similar to \code{NULL}, that
+  indicates the calling function should just use the
+  default value.  It is used in certain functions to
+  distinguish between displaying nothing (\code{NULL}) and
+  displaying a default value calculated elsewhere
+  (\code{waiver()})
+}
+\keyword{internal}
+