resolve merge conflict

Merge branch 'main' into S7_objects

# Conflicts:
#	R/aes.R
#	R/layer.R
#	R/plot-build.R
#	R/theme.R

Author: teunbrand

DESCRIPTION

@@ -249,6 +249,7 @@ Collate:
     'stat-bindot.R'
     'stat-binhex.R'
     'stat-boxplot.R'
+    'stat-connect.R'
     'stat-contour.R'
     'stat-count.R'
     'stat-density-2d.R'

NAMESPACE

@@ -238,6 +238,7 @@ export(StatBin2d)
 export(StatBindot)
 export(StatBinhex)
 export(StatBoxplot)
+export(StatConnect)
 export(StatContour)
 export(StatContourFilled)
 export(StatCount)
@@ -670,6 +671,7 @@ export(stat_bin_2d)
 export(stat_bin_hex)
 export(stat_binhex)
 export(stat_boxplot)
+export(stat_connect)
 export(stat_contour)
 export(stat_contour_filled)
 export(stat_count)
@@ -727,7 +729,6 @@ 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

@@ -1,5 +1,19 @@
 # ggplot2 (development version)
 
+* `position_fill()` avoids stacking observations of zero (@teunbrand, #6338)
+* New `layer(layout)` argument to interact with facets (@teunbrand, #3062)
+* New `stat_connect()` to connect points via steps or other shapes 
+  (@teunbrand, #6228)
+* Fixed regression with incorrectly drawn gridlines when using `coord_flip()` 
+  (@teunbrand, #6293).
+* Deprecated functions and arguments prior to ggplot2 3.0.0 throw errors instead 
+  of warnings. 
+* Functions and arguments that were soft-deprecated up to ggplot2 3.4.0 now 
+  throw warnings.
+* (internal) layer data can be attenuated with parameter attributes 
+  (@teunbrand, #3175).
+* Date scales silently coerce <POSIXct> to <Date> and datetime scales silently
+  coerce <Date> to <POSIXct> (@laurabrianna, #3533)
 * New parameters for `geom_label()` (@teunbrand and @steveharoz, #5365):
   * The `linewidth` aesthetic is now applied and replaces the `label.size` 
     argument.
@@ -239,8 +253,8 @@
   and (non-text) margins inherit from (@teunbrand, #5622).
 * `geom_ribbon()` can have varying `fill` or `alpha` in linear coordinate
   systems (@teunbrand, #4690).
-* `geom_tile()` computes default widths and heights per panel instead of
-  per layer (@teunbrand, #5740).
+* `geom_tile()` and `position_jitter()` computes default widths and heights 
+  per panel instead of per layer (@teunbrand, #5740, #3722).
 * The `fill` of the `panel.border` theme setting is ignored and forced to be
   transparent (#5782).
 * `stat_align()` skips computation when there is only 1 group and therefore
@@ -270,8 +284,11 @@
   is setup once in total instead of once per group (@teunbrand, #5971)
 * `facet_grid(space = "free")` can now be combined with `coord_fixed()` 
   (@teunbrand, #4584).
-* `theme_classic()` now has black ticks and text instead of dark gray. In 
-  addition, `theme_classic()`'s axis line end is `"square"` (@teunbrand, #5978).
+* `theme_classic()` has the following changes (@teunbrand, #5978 & #6320):
+    * Axis ticks are now black (`ink`-coloured) instead of dark gray.
+    * Axis line ends are now `"square"`.
+    * The panel grid is now blank at the `panel.grid` hierarchy level instead of 
+    the `panel.grid.major` and `panel.grid.minor` levels.
 * {tibble} is now suggested instead of imported (@teunbrand, #5986)
 * The ellipsis argument is now checked in `fortify()`, `get_alt_text()`, 
   `labs()` and several guides (@teunbrand, #3196).
@@ -308,6 +325,21 @@
   (@teunbrand, #3669). 
 * Added `scale_{x/y}_time(date_breaks, date_minor_breaks, date_labels)` 
   (@teunbrand, #4335).
+* (internal) `legend.key.width` and `legend.key.height` calculations are no
+  longer precomputed before guides are drawn (@teunbrand, #6339)
+* `ggsave()` can write a multi-page pdf file when provided with a list of plots 
+  (@teunbrand, #5093).
+* (internal) When `validate_subclass()` fails to find a class directly, it tries 
+  to retrieve the class via constructor functions (@teunbrand).
+* (internal) The ViewScale class has a `make_fixed_copy()` method to permit 
+  copying trained position scales (#3441).
+* `draw_key_rect()` replaces a `NA` fill by the `colour` aesthetic and 
+  `draw_key_polygon()` has 0 linewidth as internal default (@teunbrand, #5385).
+* Improved consistency of curve direction in `geom_curve()` (@teunbrand, #5069)
+* `linetype = NA` is now interpreted to mean 'no line' instead of raising errors
+  (@teunbrand, #6269).
+* The default colour and fill scales have a new `palette` argument 
+  (@teunbrand, #6064).
 
 # ggplot2 3.5.1
 

R/aes.R

@@ -280,7 +280,7 @@ is_position_aes <- function(vars) {
 #'
 #' @export
 aes_ <- function(x, y, ...) {
-  deprecate_soft0(
+  deprecate_warn0(
     "3.0.0",
     "aes_()",
     details = "Please use tidy evaluation idioms with `aes()`"
@@ -307,7 +307,7 @@ aes_ <- function(x, y, ...) {
 #' @rdname aes_
 #' @export
 aes_string <- function(x, y, ...) {
-  deprecate_soft0(
+  deprecate_warn0(
     "3.0.0",
     "aes_string()",
     details = c(
@@ -348,7 +348,9 @@ aes_all <- function(vars) {
 
   # Quosure the symbols in the empty environment because they can only
   # refer to the data mask
-  class_mapping(lapply(vars, function(x) new_quosure(as.name(x), emptyenv())))
+  x <- class_mapping(lapply(vars, function(x) new_quosure(as.name(x), emptyenv())))
+  class(x) <- union("unlabelled", class(x))
+  x
 }
 
 #' Automatic aesthetic mapping
@@ -361,29 +363,7 @@ aes_all <- function(vars) {
 #' @keywords internal
 #' @export
 aes_auto <- function(data = NULL, ...) {
-  deprecate_warn0("2.0.0", "aes_auto()")
-
-  # detect names of data
-  if (is.null(data)) {
-    cli::cli_abort("{.fn aes_auto} requires a {.cls data.frame} or names of data.frame.")
-  } else if (is.data.frame(data)) {
-    vars <- names(data)
-  } else {
-    vars <- data
-  }
-
-  # automatically detected aes
-  vars <- intersect(ggplot_global$all_aesthetics, vars)
-  names(vars) <- vars
-  aes <- lapply(vars, function(x) parse(text = x)[[1]])
-
-  # explicitly defined aes
-  if (length(match.call()) > 2) {
-    args <- as.list(match.call()[-1])
-    aes <- c(aes, args[names(args) != "data"])
-  }
-
-  class_mapping(rename_aes(aes))
+  lifecycle::deprecate_stop("2.0.0", "aes_auto()")
 }
 
 mapped_aesthetics <- function(x) {

R/annotation-custom.R

@@ -80,7 +80,7 @@ GeomCustomAnn <- ggproto("GeomCustomAnn", Geom,
     editGrob(grob, vp = vp, name = paste(grob$name, annotation_id()))
   },
 
-  default_aes = aes_(xmin = -Inf, xmax = Inf, ymin = -Inf, ymax = Inf)
+  default_aes = aes(xmin = -Inf, xmax = Inf, ymin = -Inf, ymax = Inf)
 )
 
 annotation_id <- local({

R/annotation-logticks.R

@@ -229,7 +229,7 @@ GeomLogticks <- ggproto("GeomLogticks", Geom,
   },
 
   default_aes = aes(
-    colour = from_theme(ink),
+    colour = from_theme(colour %||% ink),
     linewidth = from_theme(linewidth),
     linetype = from_theme(linetype),
     alpha = 1

R/bin.R

@@ -240,18 +240,24 @@ bin_loc <- function(x, id) {
   )
 }
 
-fix_bin_params = function(params, fun, version) {
+fix_bin_params <- function(params, fun, version) {
+
+  if (package_version(version) < "3.0.0") {
+    deprecate <- lifecycle::deprecate_stop
+  } else {
+    deprecate <- deprecate_warn0
+  }
 
   if (!is.null(params$origin)) {
     args <- paste0(fun, c("(origin)", "(boundary)"))
-    deprecate_warn0(version, args[1], args[2])
-    params$boudnary <- params$origin
+    deprecate(version, args[1], args[2])
+    params$boundary <- params$origin
     params$origin <- NULL
   }
 
   if (!is.null(params$right)) {
     args <- paste0(fun, c("(right)", "(closed)"))
-    deprecate_warn0(version, args[1], args[2])
+    deprecate(version, args[1], args[2])
     params$closed <- if (isTRUE(params$right)) "right" else "left"
     params$right <- NULL
   }

R/facet-.R

@@ -872,3 +872,95 @@ censor_labels <- function(ranges, layout, labels) {
   }
   ranges
 }
+
+map_facet_data <- function(data, layout, params) {
+
+  if (empty(data)) {
+    return(vec_cbind(data %|W|% NULL, PANEL = integer(0)))
+  }
+
+  vars <- params$facet %||% c(params$rows, params$cols)
+
+  if (length(vars) == 0) {
+    data$PANEL <- layout$PANEL
+    return(data)
+  }
+
+  grid_layout <- all(c("rows", "cols") %in% names(params))
+  layer_layout <- attr(data, "layout")
+  if (identical(layer_layout, "fixed")) {
+    n <- vec_size(data)
+    data <- vec_rep(data, vec_size(layout))
+    data$PANEL <- vec_rep_each(layout$PANEL, n)
+    return(data)
+  }
+
+  # Compute faceting values
+  facet_vals <- eval_facets(vars, data, params$.possible_columns)
+
+  include_margins <- !isFALSE(params$margin %||% FALSE) &&
+    nrow(facet_vals) == nrow(data) && grid_layout
+  if (include_margins) {
+    # Margins are computed on evaluated faceting values (#1864).
+    facet_vals <- reshape_add_margins(
+      vec_cbind(facet_vals, .index = seq_len(nrow(facet_vals))),
+      list(intersect(names(params$rows), names(facet_vals)),
+           intersect(names(params$cols), names(facet_vals))),
+      params$margins %||% FALSE
+    )
+    # Apply recycling on original data to fit margins
+    # We're using base subsetting here because `data` might have a superclass
+    # that isn't handled well by vctrs::vec_slice
+    data <- data[facet_vals$.index, , drop = FALSE]
+    facet_vals$.index <- NULL
+  }
+
+  # If we need to fix rows or columns, we make the corresponding faceting
+  # variables missing on purpose
+  if (grid_layout) {
+    if (identical(layer_layout, "fixed_rows")) {
+      facet_vals <- facet_vals[setdiff(names(facet_vals), names(params$cols))]
+    }
+    if (identical(layer_layout, "fixed_cols")) {
+      facet_vals <- facet_vals[setdiff(names(facet_vals), names(params$rows))]
+    }
+  }
+
+  # If any faceting variables are missing, add them in by
+  # duplicating the data
+  missing_facets <- setdiff(names(vars), names(facet_vals))
+  if (length(missing_facets) > 0) {
+
+    to_add <- unique0(layout[missing_facets])
+
+    data_rep  <- rep.int(seq_len(nrow(data)), nrow(to_add))
+    facet_rep <- rep(seq_len(nrow(to_add)), each = nrow(data))
+
+    data <- unrowname(data[data_rep, , drop = FALSE])
+    facet_vals <- unrowname(vec_cbind(
+      unrowname(facet_vals[data_rep, , drop = FALSE]),
+      unrowname(to_add[facet_rep, , drop = FALSE])
+    ))
+  }
+
+  if (nrow(facet_vals) < 1) {
+    # Add PANEL variable
+    data$PANEL <- NO_PANEL
+    return(data)
+  }
+
+  facet_vals[] <- lapply(facet_vals, as_unordered_factor)
+  facet_vals[] <- lapply(facet_vals, addNA, ifany = TRUE)
+  layout[] <- lapply(layout, as_unordered_factor)
+
+  # Add PANEL variable
+  keys <- join_keys(facet_vals, layout, by = names(vars))
+  data$PANEL <- layout$PANEL[match(keys$x, keys$y)]
+
+  # Filter panels when layer_layout is an integer
+  if (is_integerish(layer_layout)) {
+    data <- vec_slice(data, data$PANEL %in% layer_layout)
+  }
+
+  data
+}