resolve merge conflict

Merge branch 'main' into scale_name_function

# Conflicts:
#	R/labels.R

Author: teunbrand

DESCRIPTION

@@ -44,6 +44,7 @@ Imports:
     vctrs (>= 0.6.0),
     withr (>= 2.5.0)
 Suggests:
+    broom,
     covr,
     dplyr,
     ggplot2movies,
@@ -126,15 +127,15 @@ Collate:
     'facet-grid-.R'
     'facet-null.R'
     'facet-wrap.R'
-    'fortify-lm.R'
     'fortify-map.R'
-    'fortify-multcomp.R'
+    'fortify-models.R'
     'fortify-spatial.R'
     'fortify.R'
     'stat-.R'
     'geom-abline.R'
     'geom-rect.R'
     'geom-bar.R'
+    'geom-tile.R'
     'geom-bin2d.R'
     'geom-blank.R'
     'geom-boxplot.R'
@@ -167,7 +168,6 @@ Collate:
     'geom-smooth.R'
     'geom-spoke.R'
     'geom-text.R'
-    'geom-tile.R'
     'geom-violin.R'
     'geom-vline.R'
     'ggplot2-package.R'
@@ -242,6 +242,7 @@ Collate:
     'scales-.R'
     'stat-align.R'
     'stat-bin.R'
+    'stat-summary-2d.R'
     'stat-bin2d.R'
     'stat-bindot.R'
     'stat-binhex.R'
@@ -254,6 +255,7 @@ Collate:
     'stat-ellipse.R'
     'stat-function.R'
     'stat-identity.R'
+    'stat-manual.R'
     'stat-qq-line.R'
     'stat-qq.R'
     'stat-quantilemethods.R'
@@ -262,7 +264,6 @@ Collate:
     'stat-smooth-methods.R'
     'stat-smooth.R'
     'stat-sum.R'
-    'stat-summary-2d.R'
     'stat-summary-bin.R'
     'stat-summary-hex.R'
     'stat-summary.R'
@@ -273,6 +274,7 @@ Collate:
     'theme.R'
     'theme-defaults.R'
     'theme-current.R'
+    'theme-sub.R'
     'utilities-break.R'
     'utilities-grid.R'
     'utilities-help.R'

NAMESPACE

@@ -94,6 +94,7 @@ S3method(makeContext,dotstackGrob)
 S3method(merge_element,default)
 S3method(merge_element,element)
 S3method(merge_element,element_blank)
+S3method(merge_element,margin)
 S3method(pattern_alpha,GridPattern)
 S3method(pattern_alpha,GridTilingPattern)
 S3method(pattern_alpha,default)
@@ -172,6 +173,7 @@ export(GeomAbline)
 export(GeomAnnotationMap)
 export(GeomArea)
 export(GeomBar)
+export(GeomBin2d)
 export(GeomBlank)
 export(GeomBoxplot)
 export(GeomCol)
@@ -263,6 +265,7 @@ export(StatEcdf)
 export(StatEllipse)
 export(StatFunction)
 export(StatIdentity)
+export(StatManual)
 export(StatQq)
 export(StatQqLine)
 export(StatQuantile)
@@ -493,6 +496,8 @@ export(layer_sf)
 export(lims)
 export(map_data)
 export(margin)
+export(margin_auto)
+export(margin_part)
 export(max_height)
 export(max_width)
 export(mean_cl_boot)
@@ -687,6 +692,7 @@ export(stat_ecdf)
 export(stat_ellipse)
 export(stat_function)
 export(stat_identity)
+export(stat_manual)
 export(stat_qq)
 export(stat_qq_line)
 export(stat_quantile)
@@ -719,7 +725,19 @@ export(theme_linedraw)
 export(theme_minimal)
 export(theme_replace)
 export(theme_set)
+export(theme_sub_axis)
+export(theme_sub_axis_bottom)
+export(theme_sub_axis_left)
+export(theme_sub_axis_right)
+export(theme_sub_axis_top)
+export(theme_sub_axis_x)
+export(theme_sub_axis_y)
+export(theme_sub_legend)
+export(theme_sub_panel)
+export(theme_sub_plot)
+export(theme_sub_strip)
 export(theme_test)
+export(theme_transparent)
 export(theme_update)
 export(theme_void)
 export(transform_position)

NEWS.md

@@ -2,6 +2,52 @@
 
 * Scale names, guide titles and aesthetic labels can now accept functions 
   (@teunbrand, #4313)
+* Binned scales with zero-width data expand the default limits by 0.1 
+  (@teunbrand, #5066)
+* New default `geom_qq_line(geom = "abline")` for better clipping in the 
+  vertical direction. In addition, `slope` and `intercept` are new computed
+  variables in `stat_qq_line()` (@teunbrand, #6087).
+* Position adjustments can now have auxiliary aesthetics (@teunbrand).
+    * `position_nudge()` gains `nudge_x` and `nudge_y` aesthetics (#3026, #5445).
+    * `position_dodge()` gains `order` aesthetic (#3022, #3345)
+* More stability for vctrs-based palettes (@teunbrand, #6117).
+* Fixed regression in `guide_bins(reverse = TRUE)` (@teunbrand, #6183).
+* New function family for setting parts of a theme. For example, you can now use 
+  `theme_sub_axis(line, text, ticks, ticks.length, line)` as a substitute for
+  `theme(axis.line, axis.text, axis.ticks, axis.ticks.length, axis.line)`. This
+  should allow slightly terser and more organised theme declarations 
+  (@teunbrand, #5301).
+* `scale_{x/y}_discrete(continuous.limits)` is a new argument to control the
+  display range of discrete scales (@teunbrand, #4174, #6259).
+* `geom_ribbon()` now appropriately warns about, and removes, missing values 
+  (@teunbrand, #6243).
+* `guide_*()` can now accept two inside legend theme elements:
+  `legend.position.inside` and `legend.justification.inside`, allowing inside
+  legends to be placed at different positions. Only inside legends with the same
+  position and justification will be merged (@Yunuuuu, #6210).
+* New stat: `stat_manual()` for arbitrary computations (@teunbrand, #3501)
+* Reversal of a dimension, typically 'x' or 'y', is now controlled by the 
+  `reverse` argument in `coord_cartesian()`, `coord_fixed()`, `coord_radial()`
+  and `coord_sf()`. In `coord_radial()`, this replaces the older `direction` 
+  argument (#4021, @teunbrand).
+* `coord_radial()` displays minor gridlines now (@teunbrand).
+* (internal) `continuous_scale()` and `binned_scale()` sort the `limits` 
+  argument internally (@teunbrand).
+* Theme margins can have NA-units to inherit from parent elements. The new
+  function `margin_part()` has NA-units as default (@teunbrand, #6115)
+* New `margin_auto()` specification for theme margins.
+* New argument `labs(dictionary)` to label based on variable name rather than 
+  based on aesthetic (@teunbrand, #5178)
+* Fixed bug in out-of-bounds binned breaks (@teunbrand, #6054)
+* Binned guides now accept expressions as labels (@teunbrand, #6005)
+* (internal) `Scale$get_labels()` format expressions as lists.
+* In non-orthogonal coordinate systems (`coord_sf()`, `coord_polar()` and 
+  `coord_radial()`), using 'AsIs' variables escape transformation when
+  both `x` and `y` is an 'AsIs' variable (@teunbrand, #6205).
+* The following methods have been deprecated: `fortify.lm()`, `fortify.glht()`,
+  `fortify.confint.glht()`, `fortify.summary.glht()` and `fortify.cld()`. It
+  is recommend to use `broom::augment()` and `broom::tidy()` instead 
+  (@teunbrand, #3816).
 * Custom and raster annotation now respond to scale transformations, and can
   use AsIs variables for relative placement (@teunbrand based on 
   @yutannihilation's prior work, #3120)
@@ -17,6 +63,13 @@
   (@teunbrand, #4320)
 * `geom_boxplot()` gains additional arguments to style the colour, linetype and
   linewidths of the box, whiskers, median line and staples (@teunbrand, #5126)
+* `geom_violin()` gains additional arguments to style the colour, linetype and
+  linewidths of the quantiles, which replace the now-deprecated `draw_quantiles` 
+  argument (#5912).
+* (breaking) `geom_violin(quantiles)` now has actual quantiles based on
+  the data, rather than inferred quantiles based on the computed density. The
+  `quantiles` parameter that replaces `draw_quantiles` now belongs to 
+  `stat_ydensity()` instead of `geom_violin()` (@teunbrand, #4120).
 * (internal) Using `after_scale()` in the `Geom*$default_aes()` field is now
   evaluated in the context of data (@teunbrand, #6135)
 * Fixed bug where binned scales wouldn't simultaneously accept transformations
@@ -205,8 +258,28 @@
 * The ellipsis argument is now checked in `fortify()`, `get_alt_text()`, 
   `labs()` and several guides (@teunbrand, #3196).
 * `stat_summary_bin()` no longer ignores `width` parameter (@teunbrand, #4647).
-* Added `keep.zeroes` argument to `stat_bin()` (@teunbrand, #3449)
+* Reintroduced `drop` argument to `stat_bin()` (@teunbrand, #3449)
+* (internal) removed barriers for using 2D structures as aesthetics 
+  (@teunbrand, #4189).
 * `coord_sf()` no longer errors when dealing with empty graticules (@teunbrand, #6052)
+* Added `theme_transparent()` with transparent backgrounds (@topepo).
+* New theme elements `palette.{aes}.discrete` and `palette.{aes}.continuous`. 
+  Theme palettes replace palettes in scales where `palette = NULL`, which is 
+  the new default in many scales (@teunbrand, #4696).
+* `guide_axis()` no longer reserves space for blank ticks 
+  (@teunbrand, #4722, #6069).
+* `geom_abline()` clips to the panel range in the vertical direction too
+  (@teunbrand, #6086).
+* Added `panel.widths` and `panel.heights` to `theme()` (#5338, @teunbrand).
+* Standardised the calculation of `width`, which are now implemented as
+  aesthetics (@teunbrand, #2800).
+* Stricter check on `register_theme_elements(element_tree)` (@teunbrand, #6162)
+* Added `weight` aesthetic for `stat_ellipse()` (@teunbrand, #5272)
+* Fixed a bug where the `guide_custom(order)` wasn't working (@teunbrand, #6195)
+* All binning stats now use the `boundary`/`center` parametrisation rather
+  than `origin`, following in `stat_bin()`'s footsteps (@teunbrand).
+* `stat_summary_2d()` and `stat_bin_2d()` now deal with zero-range data
+  more elegantly (@teunbrand, #6207).
 
 # ggplot2 3.5.1
 

R/aes.R

@@ -38,6 +38,13 @@ NULL
 #'
 #'   [Delayed evaluation][aes_eval] for working with computed variables.
 #'
+#' @note
+#' Using `I()` to create objects of class 'AsIs' causes scales to ignore the
+#' variable and assumes the wrapped variable is direct input for the grid
+#' package. Please be aware that variables are sometimes combined, like in
+#' some stats or position adjustments, that may yield unexpected results with
+#' 'AsIs' variables.
+#'
 #' @family aesthetics documentation
 #' @return A list with class `uneval`. Components of the list are either
 #'   quosures or constants.

R/bin.R

@@ -54,19 +54,12 @@ bin_breaks <- function(breaks, closed = c("right", "left")) {
 
 bin_breaks_width <- function(x_range, width = NULL, center = NULL,
                              boundary = NULL, closed = c("right", "left")) {
-  check_length(x_range, 2L)
 
-  # binwidth seems to be the argument name supplied to width. (stat-bin and stat-bindot)
-  check_number_decimal(width, min = 0, allow_infinite = FALSE, arg = "binwidth")
-
-  if (!is.null(boundary) && !is.null(center)) {
-    cli::cli_abort("Only one of {.arg boundary} and {.arg center} may be specified.")
-  } else if (is.null(boundary)) {
+  if (is.null(boundary)) {
     if (is.null(center)) {
       # If neither edge nor center given, compute both using tile layer's
       # algorithm. This puts min and max of data in outer half of their bins.
       boundary <- width / 2
-
     } else {
       # If center given but not boundary, compute boundary.
       boundary <- center - width / 2
@@ -75,9 +68,6 @@ bin_breaks_width <- function(x_range, width = NULL, center = NULL,
 
   # Find the left side of left-most bin: inputs could be Dates or POSIXct, so
   # coerce to numeric first.
-  x_range <- as.numeric(x_range)
-  width <- as.numeric(width)
-  boundary <- as.numeric(boundary)
   shift <- floor((x_range[1] - boundary) / width)
   origin <- boundary + shift * width
 
@@ -104,9 +94,7 @@ bin_breaks_width <- function(x_range, width = NULL, center = NULL,
 
 bin_breaks_bins <- function(x_range, bins = 30, center = NULL,
                             boundary = NULL, closed = c("right", "left")) {
-  check_length(x_range, 2L)
 
-  check_number_whole(bins, min = 1)
   if (zero_range(x_range)) {
     # 0.1 is the same width as the expansion `default_expansion()` gives for 0-width data
     width <- 0.1
@@ -128,6 +116,56 @@ bin_breaks_bins <- function(x_range, bins = 30, center = NULL,
 
 # Compute bins ------------------------------------------------------------
 
+compute_bins <- function(x, scale = NULL, breaks = NULL, binwidth = NULL, bins = NULL,
+                         center = NULL, boundary = NULL,
+                         closed = c("right", "left")) {
+
+  range <- if (is.scale(scale)) scale$dimension() else range(x)
+  check_length(range, 2L)
+
+  if (!is.null(breaks)) {
+    breaks <- allow_lambda(breaks)
+    if (is.function(breaks)) {
+      breaks <- breaks(x)
+    }
+    if (is.scale(scale) && !scale$is_discrete()) {
+      breaks <- scale$transform(breaks)
+    }
+    check_numeric(breaks)
+    bins <- bin_breaks(breaks, closed)
+    return(bins)
+  }
+
+  check_number_decimal(boundary, allow_infinite = FALSE, allow_null = TRUE)
+  check_number_decimal(center, allow_infinite = FALSE, allow_null = TRUE)
+  if (!is.null(boundary) && !is.null(center)) {
+    cli::cli_abort("Only one of {.arg boundary} and {.arg center} may be specified.")
+  }
+
+  if (!is.null(binwidth)) {
+    binwidth <- allow_lambda(binwidth)
+    if (is.function(binwidth)) {
+      binwidth <- binwidth(x)
+    }
+    check_number_decimal(binwidth, min = 0, allow_infinite = FALSE)
+    bins <- bin_breaks_width(
+      range, binwidth,
+      center = center, boundary = boundary, closed = closed
+    )
+    return(bins)
+  }
+
+  bins <- allow_lambda(bins)
+  if (is.function(bins)) {
+    bins <- bins(x)
+  }
+  check_number_whole(bins, min = 1, allow_infinite = FALSE)
+  bin_breaks_bins(
+    range, bins,
+    center = center, boundary = boundary, closed = closed
+  )
+}
+
 bin_vector <- function(x, bins, weight = NULL, pad = FALSE) {
   check_object(bins, is_bins, "a {.cls ggplot2_bins} object")
 
@@ -141,8 +179,7 @@ bin_vector <- function(x, bins, weight = NULL, pad = FALSE) {
     weight[is.na(weight)] <- 0
   }
 
-  bin_idx <- cut(x, bins$fuzzy, right = bins$right_closed,
-    include.lowest = TRUE)
+  bin_idx <- bin_cut(x, bins)
   bin_count <- as.numeric(tapply(weight, bin_idx, sum, na.rm = TRUE))
   bin_count[is.na(bin_count)] <- 0
 
@@ -170,6 +207,10 @@ bin_vector <- function(x, bins, weight = NULL, pad = FALSE) {
   bin_out(bin_count, bin_x, bin_widths)
 }
 
+bin_cut <- function(x, bins) {
+  cut(x, bins$fuzzy, right = bins$right_closed, include.lowest = TRUE)
+}
+
 bin_out <- function(count = integer(0), x = numeric(0), width = numeric(0),
   xmin = x - width / 2, xmax = x + width / 2) {
   density <- count / width / sum(abs(count))
@@ -186,3 +227,41 @@ bin_out <- function(count = integer(0), x = numeric(0), width = numeric(0),
     .size = length(count)
   )
 }
+
+bin_loc <- function(x, id) {
+  left <- x[-length(x)]
+  right <- x[-1]
+
+  list(
+    left = left[id],
+    right = right[id],
+    mid = ((left + right) / 2)[id],
+    length = diff(x)[id]
+  )
+}
+
+fix_bin_params = function(params, fun, version) {
+
+  if (!is.null(params$origin)) {
+    args <- paste0(fun, c("(origin)", "(boundary)"))
+    deprecate_warn0(version, args[1], args[2])
+    params$boudnary <- params$origin
+    params$origin <- NULL
+  }
+
+  if (!is.null(params$right)) {
+    args <- paste0(fun, c("(right)", "(closed)"))
+    deprecate_warn0(version, args[1], args[2])
+    params$closed <- if (isTRUE(params$right)) "right" else "left"
+    params$right <- NULL
+  }
+
+  if (is.null(params$breaks %||% params$binwidth %||% params$bins)) {
+    cli::cli_inform(
+      "{.fn {fun}} using {.code bins = 30}. Pick better value {.arg binwidth}."
+    )
+    params$bins <- 30
+  }
+
+  params
+}