resolve merge conflict

Merge branch 'main' into internal_naming

# Conflicts:
#	R/geom-crossbar.R
#	R/geom-errorbarh.R
#	R/scale-colour.R
#	R/scale-hue.R
#	R/utilities-checks.R
#	tests/testthat/_snaps/facet-.md
#	tests/testthat/test-ggsave.R

Author: teunbrand

.github/workflows/R-CMD-check.yaml

@@ -63,7 +63,7 @@ jobs:
           cache-version: 3
           extra-packages: >
             any::rcmdcheck,
-            Hmisc=?ignore-before-r=4.1.0,
+            Hmisc=?ignore-before-r=4.2.0,
             quantreg=?ignore-before-r=4.3.0
           needs: check
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ggplot2
-Version: 3.5.1.9000
 Title: Create Elegant Data Visualisations Using the Grammar of Graphics
+Version: 3.5.1.9000
 Authors@R: c(
     person("Hadley", "Wickham", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0003-4757-117X")),
@@ -30,21 +30,21 @@ License: MIT + file LICENSE
 URL: https://ggplot2.tidyverse.org, https://github.com/tidyverse/ggplot2
 BugReports: https://github.com/tidyverse/ggplot2/issues
 Depends:
-    R (>= 3.5)
+    R (>= 4.0)
 Imports: 
     cli,
     grDevices,
     grid,
     gtable (>= 0.1.1),
     isoband,
     lifecycle (> 1.0.1),
-    MASS,
     rlang (>= 1.1.0),
     scales (>= 1.3.0),
     stats,
     vctrs (>= 0.6.0),
     withr (>= 2.5.0)
 Suggests:
+    broom,
     covr,
     dplyr,
     ggplot2movies,
@@ -53,6 +53,7 @@ Suggests:
     knitr,
     mapproj,
     maps,
+    MASS,
     mgcv,
     multcomp,
     munsell,
@@ -75,6 +76,7 @@ VignetteBuilder:
     knitr
 Config/Needs/website: ggtext, tidyr, forcats, tidyverse/tidytemplate
 Config/testthat/edition: 3
+Config/usethis/last-upkeep: 2024-10-24
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
@@ -125,15 +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'
@@ -150,7 +152,6 @@ Collate:
     'geom-density2d.R'
     'geom-dotplot.R'
     'geom-errorbar.R'
-    'geom-errorbarh.R'
     'geom-freqpoly.R'
     'geom-function.R'
     'geom-hex.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'
@@ -254,6 +254,7 @@ Collate:
     'stat-ellipse.R'
     'stat-function.R'
     'stat-identity.R'
+    'stat-manual.R'
     'stat-qq-line.R'
     'stat-qq.R'
     'stat-quantilemethods.R'

LICENSE.md

@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) 2020 ggplot2 authors
+Copyright (c) 2024 ggplot2 core developer team
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

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)
@@ -461,7 +464,6 @@ export(guides)
 export(has_flipped_aes)
 export(is.Coord)
 export(is.coord)
-export(is.element)
 export(is.facet)
 export(is.geom)
 export(is.ggplot)
@@ -475,6 +477,8 @@ export(is.position)
 export(is.scale)
 export(is.stat)
 export(is.theme)
+export(is.theme_element)
+export(is.waiver)
 export(label_both)
 export(label_bquote)
 export(label_context)
@@ -492,6 +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)
@@ -686,6 +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)
@@ -719,6 +726,7 @@ export(theme_minimal)
 export(theme_replace)
 export(theme_set)
 export(theme_test)
+export(theme_transparent)
 export(theme_update)
 export(theme_void)
 export(transform_position)

NEWS.md

@@ -1,5 +1,53 @@
 # ggplot2 (development version)
 
+* `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$get_labels()` format expressions as lists.
+* In non-orthogonal coordinate systems (`coord_sf()`, `coord_polar()` and 
+  `coord_radial()`), using 'AsIs' variables escape transformation when
+  both `x` and `y` is an 'AsIs' variable (@teunbrand, #6205).
+* The following methods have been deprecated: `fortify.lm()`, `fortify.glht()`,
+  `fortify.confint.glht()`, `fortify.summary.glht()` and `fortify.cld()`. It
+  is recommend to use `broom::augment()` and `broom::tidy()` instead 
+  (@teunbrand, #3816).
+* Custom and raster annotation now respond to scale transformations, and can
+  use AsIs variables for relative placement (@teunbrand based on 
+  @yutannihilation's prior work, #3120)
+* When discrete breaks have names, they'll be used as labels by default 
+  (@teunbrand, #6147).
+* The helper function `is.waiver()` is now exported to help extensions to work
+  with `waiver()` objects (@arcresu, #6173).
+* Date(time) scales now throw appropriate errors when `date_breaks`, 
+  `date_minor_breaks` or `date_labels` are not strings (@RodDalBen, #5880)
+* `geom_errorbarh()` is deprecated in favour of 
+  `geom_errorbar(orientation = "y")` (@teunbrand, #5961).
+* `geom_contour()` should be able to recognise a rotated grid of points 
+  (@teunbrand, #4320)
+* `geom_boxplot()` gains additional arguments to style the colour, linetype and
+  linewidths of the box, whiskers, median line and staples (@teunbrand, #5126)
+* (internal) Using `after_scale()` in the `Geom*$default_aes()` field is now
+  evaluated in the context of data (@teunbrand, #6135)
+* Fixed bug where binned scales wouldn't simultaneously accept transformations
+  and function-limits (@teunbrand, #6144).
+* Fixed bug where the `ggplot2::`-prefix did not work with `stage()` 
+  (@teunbrand, #6104).
 * New `get_labs()` function for retrieving completed plot labels 
   (@teunbrand, #6008).
 * Built-in `theme_*()` functions now have `ink` and `paper` arguments to control
@@ -182,6 +230,19 @@
 * 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)
+* (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).
 
 # ggplot2 3.5.1
 
@@ -228,6 +289,7 @@ documentation updates.
 * `annotate()` now warns about `stat` or `position` arguments (@teunbrand, #5151)
 * `guide_coloursteps(even.steps = FALSE)` now works with discrete data that has 
   been formatted by `cut()` (@teunbrand, #3877).
+* `ggsave()` now offers to install svglite if needed (@eliocamp, #6166).
 
 # ggplot2 3.5.0
 

R/aes-evaluation.R

@@ -32,7 +32,7 @@
 #' Below follows an overview of the three stages of evaluation and how aesthetic
 #' evaluation can be controlled.
 #'
-#' ## Stage 1: direct input
+#' ## Stage 1: direct input at the start
 #' The default is to map at the beginning, using the layer data provided by
 #' the user. If you want to map directly from the layer data you should not do
 #' anything special. This is the only stage where the original layer data can
@@ -87,17 +87,19 @@
 #' ```
 #'
 #' ## Complex staging
-#' If you want to map the same aesthetic multiple times, e.g. map `x` to a
-#' data column for the stat, but remap it for the geom, you can use the
-#' `stage()` function to collect multiple mappings.
+#' Sometimes, you may want to map the same aesthetic multiple times, e.g. map
+#' `x` to a data column at the start for the layer stat, but remap it later to
+#' a variable from the stat transformation for the layer geom. The `stage()`
+#' function allows you to control multiple mappings for the same aesthetic
+#' across all three stages of evaluation.
 #'
 #' ```r
 #' # Use stage to modify the scaled fill
 #' ggplot(mpg, aes(class, hwy)) +
 #'   geom_boxplot(aes(fill = stage(class, after_scale = alpha(fill, 0.4))))
 #'
 #' # Using data for computing summary, but placing label elsewhere.
-#' # Also, we're making our own computed variable to use for the label.
+#' # Also, we're making our own computed variables to use for the label.
 #' ggplot(mpg, aes(class, displ)) +
 #'   geom_violin() +
 #'   stat_summary(
@@ -110,6 +112,11 @@
 #'   )
 #' ```
 #'
+#' Conceptually, `aes(x)` is equivalent to `aes(stage(start = x))`, and
+#' `aes(after_stat(count))` is equivalent to `aes(stage(after_stat = count))`,
+#' and so on. `stage()` is most useful when at least two of its arguments are
+#' specified.
+#'
 #' ## Theme access
 #' The `from_theme()` function can be used to acces the [`element_geom()`]
 #' fields of the `theme(geom)` argument. Using `aes(colour = from_theme(ink))`
@@ -332,7 +339,7 @@ strip_stage <- function(expr) {
   } else if (is_call(uq_expr, "stage")) {
     uq_expr <- call_match(uq_expr, stage)
     # Prefer stat mapping if present, otherwise original mapping (fallback to
-    # scale mapping) but there should always be two arguments to stage()
+    # scale mapping)
     uq_expr$after_stat %||% uq_expr$start %||% uq_expr$after_scale
   } else {
     expr
@@ -358,3 +365,39 @@ make_labels <- function(mapping) {
   }
   Map(default_label, names(mapping), mapping)
 }
+
+eval_aesthetics <- function(aesthetics, data, mask = NULL) {
+
+  env <- child_env(base_env())
+
+  # Here we mask functions, often to replace `stage()` with context appropriate
+  # functions `stage_calculated()`/`stage_scaled()`.
+  if (length(mask) > 0) {
+    aesthetics <- substitute_aes(aesthetics, mask_function, mask = mask)
+  }
+
+  evaled <- lapply(aesthetics, eval_tidy, data = data, env = env)
+  names(evaled) <- names(aesthetics)
+  compact(rename_aes(evaled))
+}
+
+# `mask` is a list of functions where `names(mask)` indicate names of functions
+# that need to be replaced, and `mask[[i]]` is the function to replace it
+# with.
+mask_function <- function(x, mask) {
+  if (!is.call(x)) {
+    return(x)
+  }
+  nms <- names(mask)
+  x[-1] <- lapply(x[-1], mask_function, mask = mask)
+  if (!is_call(x, nms)) {
+    return(x)
+  }
+  for (nm in nms) {
+    if (is_call(x, nm)) {
+      x[[1]] <- mask[[nm]]
+      return(x)
+    }
+  }
+}
+

R/aes.R

@@ -198,9 +198,12 @@ rename_aes <- function(x) {
   }
   x
 }
-substitute_aes <- function(x) {
+
+# `x` is assumed to be a strict list of quosures;
+# it should have no non-quosure constants in it, even though `aes()` allows it.
+substitute_aes <- function(x, fun = standardise_aes_symbols, ...) {
   x <- lapply(x, function(aesthetic) {
-    as_quosure(standardise_aes_symbols(quo_get_expr(aesthetic)), env = environment(aesthetic))
+    as_quosure(fun(quo_get_expr(aesthetic), ...), env = environment(aesthetic))
   })
   class(x) <- "uneval"
   x