Merge tag 'v1.0.0'

Release 1.0.0 of ggplot2

Conflicts:
	R/facet-labels.r
	man/labeller.Rd

Author: wch

.Rbuildignore

@@ -4,3 +4,4 @@ visual_test
 ^\.travis\.yml$
 ^/\.gitattributes$
 ^inst/web$
+^notes$

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ggplot2
 Type: Package
 Title: An implementation of the Grammar of Graphics
-Version: 0.9.3.1.99
+Version: 1.0.0
 Author: Hadley Wickham <[email protected]>, Winston Chang <[email protected]>
 Maintainer: Hadley Wickham <[email protected]>
 Description: An implementation of the grammar of graphics

NEWS

@@ -1,27 +1,7 @@
-ggplot2 0.9.3.1.99
+ggplot2 1.0.0
 ----------------------------------------------------------------
 
-* New `aes_q()` function to generate aesthetic specifications from
-  quoted calls/names. `aes_string()` uses names `x` and `y` for first
-  two unnamed arguments.
-
-* Marginal improvements to `theme_bw` and `theme_classic` (@jiho, #934)
-
-* `stat_ellipse()` adds data ellipses. It supports bivariate normal and t distributions,
-  as well as a euclidian distance circle. (@jofrhwld, #926)
-
-* Add new themes: `theme_linedraw()` is similar to `theme_bw()` but with
-  truly only white and black elements and spacing between elements identical
-  to `theme_gray`. `theme_light` is similar but with light gray box and axes
-  around the plot, to emphasise content more (@jiho, #923)
-
-* Allow to use brewer palettes for continuous scales, through the new
-  `scale_fill/colour_distiller()` functions (@jiho, #925).
-
-* `position_jitterdodge()` combines `position_jitter()` and `position_dodge()`,
-  allowing the user to plot and align points generated by e.g. `geom_point()`
-  with those generated by a dodged `geom_boxplot()`. See
-  `example(position_jitterdodge)` for a potential usage. (@kevinushey, #932)
+NEW FEATURES
 
 * New coordinate system for small scale maps. `coord_quickmap()` computes and
   sets the correct aspect ratio between one degree of latitude and one degree
@@ -34,22 +14,27 @@ ggplot2 0.9.3.1.99
   the width of boxplots should be proportional to the size of the groups
   (@tsieger, #927).
 
+* `position_jitterdodge()` combines `position_jitter()` and `position_dodge()`,
+  allowing the user to plot and align points generated by e.g. `geom_point()`
+  with those generated by a dodged `geom_boxplot()`. See
+  `example(position_jitterdodge)` for a potential usage. (@kevinushey, #932)
+
 * Allow specifying only one of the limits in a scale and use the automatic
   calculation of the other limit by passing NA to to the limit function,
   `xlim()` or `ylim()` (@jimhester, #557).
 
-* `geom_dotplot` now works with qplot. (@rasmusab. Fixes #825)
-
-* `stat_smooth()` checks for `method = "auto"` and `method = "glm"` in
-  a safer way.
+* Allow to use brewer palettes for continuous scales, through the new
+  `scale_fill/colour_distiller()` functions (@jiho, #925).
 
-* `ggpcp()`, `ggfluctuation()`, `ggmissing()`, `ggstructure()`, and
-  `ggorder()` are now defunct and have been removed.
+* `stat_ellipse()` adds data ellipses. It supports bivariate normal and t distributions,
+  as well as a euclidian distance circle. (@jofrhwld, #926)
 
-* `fortify.SpatialPolygonsDataFrame()` now calls `polygons` without
-  requiring the `sp` to be loaded first (@seancarmody, #879).
+* Add new themes: `theme_linedraw()` is similar to `theme_bw()` but with
+  truly only white and black elements and spacing between elements identical
+  to `theme_gray`. `theme_light` is similar but with light gray box and axes
+  around the plot, to emphasise content more (@jiho, #923)
 
-* theme: new theme settings panel.margin.x and panel.margin.y (units) allow
+* new theme settings panel.margin.x and panel.margin.y (units) allow
   specifying horizontal and vertical gap between panels in facetted plots (for
   both grid and wrap).  (Kirill Müller. Fixes #839)
 
@@ -59,23 +44,43 @@ ggplot2 0.9.3.1.99
   and `hjust` is now the same for both rotated and non-rotated text elements
   (0 = top/left, 1 = bottom/right, 0.5 = centered).  (@krlmlr, #883)
 
+* Added helper function `labeller()` for formatting faceting values.
+  (@stefanedwards, #910). Added `label_wrap_gen` based on
+  https://github.com/hadley/ggplot2/wiki/labeller#writing-new-labellers
+  (@stefanedwards, #910)
+
+BUG FIXES AND MINOR IMPROVEMENTS
+
 * `aes()` no more treats variables like `a..x..b as a calculated aesthetic.
   (@krlmlr, #834.)
 
+* New `aes_q()` function to generate aesthetic specifications from
+  quoted calls/names. `aes_string()` uses names `x` and `y` for first
+  two unnamed arguments.
+
+* `fortify.SpatialPolygonsDataFrame()` now calls `polygons` without
+  requiring the `sp` to be loaded first (@seancarmody, #879).
+
+* The outliers of `geom_boxplot()` use the default colour, size and shape from
+  `geom_point()`. Changing the defaults of `geom_point()` with
+  `update_geom_defaults()` will apply the same changes to the outliers of
+  `geom_boxplot()`. Changing the defaults for the outliers was previously not
+  possible. (@ThierryO, #757)
+
+* `geom_dotplot()` now works with `qplot()`. (@rasmusab. Fixes #825)
+
+* Marginal improvements to `theme_bw()` and `theme_classic()` (@jiho, #934)
+
+* `stat_smooth()` checks for `method = "auto"` and `method = "glm"` in
+  a safer way.
+
 * Add `"none"` to documentation of `theme()` for parameter `legend.position`
   (@krlmlr, #829).
 
-* The outliers of geom_boxplot() use the default colour, size and shape from
-  geom_point(). Changing the defaults of geom_point() with
-  update_geom_defaults() will apply the same changes to the outliers of
-  geom_boxplot(). Changing the defaults for the outliers was previously not
-  possible. (@ThierryO, #757)
-* Added helper function `labeller` for formatting faceting values.
-  (@stefanedwards, #910)
+REMOVED FUNCTIONALITY
 
-* Added `label_wrap_gen` based on 
-  https://github.com/hadley/ggplot2/wiki/labeller#writing-new-labellers
-  (@stefanedwards, #910)
+* `ggpcp()`, `ggfluctuation()`, `ggmissing()`, `ggstructure()`, and
+  `ggorder()` are now defunct and have been removed.
 
 ggplot2 0.9.3.1
 ----------------------------------------------------------------

R/aes-position.r

@@ -20,23 +20,29 @@
 #' # generate sample data
 #' library(plyr)
 #' abc <- adply(matrix(rnorm(100), ncol = 5), 2, quantile, c(0, .25, .5, .75, 1))
-#' b <- ggplot(abc, aes(x = X1, ymin = "0%", lower = "25%", middle = "50%", upper = "75%", ymax = "100%"))
+#' b <- ggplot(abc, aes(x = X1, ymin = "0%", lower = "25%",
+#'   middle = "50%", upper = "75%", ymax = "100%"))
 #' b + geom_boxplot(stat = "identity")
 #'
 #' # Using annotate
 #' p <- ggplot(mtcars, aes(wt, mpg)) + geom_point()
-#' p + annotate("rect", xmin = 2, xmax = 3.5, ymin = 2, ymax = 25, fill = "dark grey", alpha = .5)
+#' p + annotate("rect", xmin = 2, xmax = 3.5, ymin = 2, ymax = 25,
+#'   fill = "dark grey", alpha = .5)
 #'
 #' # Geom_segment examples
 #' library(grid)
-#' p + geom_segment(aes(x = 2, y = 15, xend = 2, yend = 25), arrow = arrow(length = unit(0.5, "cm")))
-#' p + geom_segment(aes(x = 2, y = 15, xend = 3, yend = 15), arrow = arrow(length = unit(0.5, "cm")))
-#' p + geom_segment(aes(x = 5, y = 30, xend = 3.5, yend = 25), arrow = arrow(length = unit(0.5, "cm")))
+#' p + geom_segment(aes(x = 2, y = 15, xend = 2, yend = 25),
+#'   arrow = arrow(length = unit(0.5, "cm")))
+#' p + geom_segment(aes(x = 2, y = 15, xend = 3, yend = 15),
+#'   arrow = arrow(length = unit(0.5, "cm")))
+#' p + geom_segment(aes(x = 5, y = 30, xend = 3.5, yend = 25),
+#'   arrow = arrow(length = unit(0.5, "cm")))
 #'
 #' # You can also use geom_segment to recreate plot(type = "h") :
 #' counts <- as.data.frame(table(x = rpois(100, 5)))
 #' counts$x <- as.numeric(as.character(counts$x))
 #' with(counts, plot(x, Freq, type = "h", lwd = 10))
 #'
-#' qplot(x, Freq, data = counts, geom = "segment", yend = 0, xend = x, size = I(10))
+#' qplot(x, Freq, data = counts, geom = "segment", yend = 0, xend = x,
+#'   size = I(10))
 NULL

R/annotation-custom.r

@@ -24,14 +24,13 @@ NULL
 #' # Dummy plot
 #' base <- qplot(1:10, 1:10, geom = "blank") + theme_bw()
 #' # Adding a table
-#' \donttest{
-#' require(gridExtra)
+#' \donttest{if (require(gridExtra)) {
 #' base + annotation_custom(grob = tableGrob(head(iris[ ,1:3])),
 #'         xmin = 3, xmax = 6, ymin = 2, ymax = 8)
 #' # full panel
 #' base + annotation_custom(grob = roundrectGrob(),
 #'           xmin = -Inf, xmax = Inf, ymin = -Inf, ymax = Inf)
-#' }
+#' }}
 #' # Inset plot
 #' g <- ggplotGrob(qplot(1, 1) +
 #'   theme(plot.background = element_rect(colour = "black")))

R/facet-labels.r

@@ -61,94 +61,88 @@ label_bquote <- function(expr = beta ^ .(x)) {
       eval(substitute(bquote(expr, list(x = x)), list(expr = quoted))))
   }
 }
+globalVariables("x")
+
 
 #' Label facets with a word wrapped label.
-#' 
+#'
 #' Uses \code{\link[base]{strwrap}} for line wrapping.
 #' @param width integer, target column width for output.
 #' @export
 #' @seealso , \code{\link{labeller}}
 label_wrap_gen <- function(width = 25) {
   function(variable, values) {
-    vapply(strwrap(as.character(values), width = width, simplify = FALSE), 
+    vapply(strwrap(as.character(values), width = width, simplify = FALSE),
            paste, vector('character', 1), collapse = "\n")
   }
 }
 
 #' Generic labeller function for facets
-#' 
+#'
 #' One-step function for providing methods or named character vectors
 #' for displaying labels in facets.
-#' 
+#'
 #' The provided methods are checked for number of arguments.
-#' If the provided method takes less than two 
-#' (e.g. \code{\link[Hmisc]{capitalize}}), 
+#' If the provided method takes less than two
+#' (e.g. \code{\link[Hmisc]{capitalize}}),
 #' the method is passed \code{values}.
-#' Else (e.g. \code{\link{label_both}}), 
+#' Else (e.g. \code{\link{label_both}}),
 #' it is passed \code{variable} and \code{values} (in that order).
 #' If you want to be certain, use e.g. an anonymous function.
-#' If errors are returned such as ``argument ".." is missing, with no default'' 
+#' If errors are returned such as ``argument ".." is missing, with no default''
 #' or ``unused argument (variable)'', matching the method's arguments does not
 #' work as expected; make a wrapper function.
-#' 
 #'
-#' @param ... Named arguments of the form \code{variable=values}, 
-#'   where \code{values} could be a vector or method.         
-#' @param keep.as.numeric logical, default TRUE. When FALSE, converts numeric 
+#'
+#' @param ... Named arguments of the form \code{variable=values},
+#'   where \code{values} could be a vector or method.
+#' @param keep.as.numeric logical, default TRUE. When FALSE, converts numeric
 #'   values supplied as margins to the facet to characters.
 #' @family facet labeller
-#' @return Function to supply to 
+#' @return Function to supply to
 #'   \code{\link{facet_grid}} for the argument \code{labeller}.
-#' @export 
+#' @export
 #' @examples
-#' 
-#' data(mpg)
-#' 
+#' \donttest{
 #' p1 <- ggplot(mpg, aes(cty, hwy)) + geom_point()
-#' 
-#' 
 #' p1 + facet_grid(cyl ~ class, labeller=label_both)
-#'   
 #' p1 + facet_grid(cyl ~ class, labeller=labeller(cyl=label_both))
-#'   
-#' ggplot(mtcars, aes(x = mpg, y = wt)) + geom_point() + 
-#'   facet_grid(vs + am ~ gear, margins=TRUE, 
+#'
+#' ggplot(mtcars, aes(x = mpg, y = wt)) + geom_point() +
+#'   facet_grid(vs + am ~ gear, margins=TRUE,
 #'              labeller=labeller(vs=label_both, am=label_both))
-#' 
-#' 
-#' 
-#' data(msleep)
+#'
 #' capitalize <- function(string) {
 #'   substr(string, 1, 1) <- toupper(substr(string, 1, 1))
-#'  string 
+#'   string
 #' }
 #' conservation_status <- c('cd'='Conservation Dependent',
-#'                          'en'='Endangered', 
+#'                          'en'='Endangered',
 #'                          'lc'='Least concern',
-#'                          'nt'='Near Threatened', 
+#'                          'nt'='Near Threatened',
 #'                          'vu'='Vulnerable',
 #'                          'domesticated'='Domesticated')
-#' ## Source: http://en.wikipedia.org/wiki/Uncyclopedia:Conservation_status 
-#'
-#' p2 <- ggplot(msleep, aes(x=sleep_total, y=awake)) + geom_point() 
-#' p2 + facet_grid(vore ~ conservation, labeller=labeller(vore=capitalize))
-#'   
-#' p2 + facet_grid(vore ~ conservation, 
-#'   labeller=labeller(vore=capitalize, conservation=conservation_status ))
-#' 
-#' # We could of course have renamed the levels; 
-#' # then we can apply another nifty function:
-#' library(plyr)
-#' msleep$conservation2 <- revalue(msleep$conservation, conservation_status)                         
-#'
-#' p2 %+% msleep + facet_grid(vore ~ conservation2, labeller=labeller(vore=capitalize))
-#' 
-#' p2 %+% msleep + facet_grid(vore ~ conservation2, 
-#'   labeller=labeller(conservation2=label_wrap_gen(10) ))
-#' 
+#' ## Source: http://en.wikipedia.org/wiki/Uncyclopedia:Conservation_status
+#'
+#' p2 <- ggplot(msleep, aes(x=sleep_total, y=awake)) + geom_point()
+#' p2 + facet_grid(vore ~ conservation, labeller = labeller(vore = capitalize))
+#'
+#' p2 + facet_grid(vore ~ conservation,
+#'   labeller=labeller(vore = capitalize, conservation = conservation_status ))
+#'
+#' # We could of course have renamed the levels;
+#' # then we can apply another nifty function
+#' msleep$conservation2 <- plyr::revalue(msleep$conservation, conservation_status)
+#'
+#' p2 %+% msleep +
+#'   facet_grid(vore ~ conservation2, labeller = labeller(vore = capitalize))
+#' p2 %+% msleep +
+#'  facet_grid(vore ~ conservation2, labeller = labeller(conservation2 =
+#'  label_wrap_gen(10)))
+#' }
 labeller <- function(..., keep.as.numeric=FALSE) {
   args <- list(...)
-  
+
   function(variable, values) {
     if (is.logical(values)) {
       values <- as.integer(values) + 1
@@ -157,27 +151,27 @@ labeller <- function(..., keep.as.numeric=FALSE) {
     } else if (is.numeric(values) & !keep.as.numeric) {
       values <- as.character(values)
     }
-      
+
     res <- args[[variable]]
-    
+
     if (is.null(res)) {
       # If the facetting margin (i.e. `variable`) was not specified when calling
       # labeller, default to use the actual values.
       result <- values
-      
+
     } else if (is.function(res)) {
       # How should `variable` and `values` be passed to a function? ------------
-      arguments <- length(formals(res))    
+      arguments <- length(formals(res))
       if (arguments < 2) {
         result <- res(values)
       } else {
         result <- res(variable, values)
-      }     
-      
+      }
+
     } else {
       result <- res[values]
     }
-    
+
     return(result)
   }
 }

R/fortify-lm.r

@@ -59,7 +59,7 @@
 #'   geom_abline(slope = seq(0, 3, by = 0.5), colour = "white") +
 #'   geom_smooth(se = FALSE) +
 #'   geom_point()
-#' qplot(.hat, .cooksd, size = .cooksd / .hat, data = mod) + scale_area()
+#' qplot(.hat, .cooksd, size = .cooksd / .hat, data = mod) + scale_size_area()
 fortify.lm <- function(model, data = model$model, ...) {
   infl <- influence(model, do.coef = FALSE)
   data$.hat <- infl$hat

R/geom-boxplot.r

@@ -92,7 +92,8 @@
 #' # Using precomputed statistics
 #' # generate sample data
 #' abc <- adply(matrix(rnorm(100), ncol = 5), 2, quantile, c(0, .25, .5, .75, 1))
-#' b <- ggplot(abc, aes(x = X1, ymin = `0%`, lower = `25%`, middle = `50%`, upper = `75%`, ymax = `100%`))
+#' b <- ggplot(abc, aes(x = X1, ymin = `0%`, lower = `25%`,
+#'    middle = `50%`, upper = `75%`, ymax = `100%`))
 #' b + geom_boxplot(stat = "identity")
 #' b + geom_boxplot(stat = "identity") + coord_flip()
 #' b + geom_boxplot(aes(fill = X1), stat = "identity")
@@ -112,7 +113,8 @@
 geom_boxplot <- function (mapping = NULL, data = NULL, stat = "boxplot",
                           position = "dodge", outlier.colour = NULL,
                           outlier.shape = NULL, outlier.size = NULL,
-                          notch = FALSE, notchwidth = .5, ...) {
+                          notch = FALSE, notchwidth = .5, varwidth = FALSE,
+                          ...) {
 
   outlier_defaults <- Geom$find('point')$default_aes()
 
@@ -123,7 +125,7 @@ geom_boxplot <- function (mapping = NULL, data = NULL, stat = "boxplot",
   GeomBoxplot$new(mapping = mapping, data = data, stat = stat,
     position = position, outlier.colour = outlier.colour,
     outlier.shape = outlier.shape, outlier.size = outlier.size, notch = notch,
-    notchwidth = notchwidth, ...)
+    notchwidth = notchwidth, varwidth = varwidth, ...)
 }
 
 GeomBoxplot <- proto(Geom, {