Merge branch 'master' into v3.2.1-rc

Author: thomasp85

.travis.yml

@@ -1,7 +1,5 @@
 language: R
 cache: packages
-sudo: true
-dist: trusty
 
 # build matrix; turn on vdiffr only on r release
 matrix:
@@ -35,8 +33,13 @@ env:
 after_success:
   - Rscript -e 'covr::codecov()'
 
-before_install:
-  - sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable --yes
-  - sudo apt-get --yes --force-yes update -qq
-  - sudo apt-get install --yes libudunits2-dev libproj-dev libgeos-dev libgdal-dev
-  - Rscript -e 'update.packages(ask = FALSE)'
+addons:
+  apt:
+    sources:
+      - sourceline: 'ppa:ubuntugis/ppa'
+    packages:
+      - libudunits2-dev
+      - libproj-dev
+      - libgeos-dev
+      - libgdal-dev
+

CONTRIBUTING.md

@@ -6,7 +6,7 @@ quickly as possible. The guide is divided into two main pieces:
 1. Filing a bug report or feature request in an issue.
 1. Suggesting a change via a pull request.
 
-Please note that ggplot2 is released with a [Contributor Code of Conduct](.github/CODE_OF_CONDUCT.md). By contributing to this project, 
+Please note that ggplot2 is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, 
 you agree to abide by its terms.
 
 ## Issues

DESCRIPTION

@@ -39,6 +39,7 @@ Suggests:
     ggplot2movies,
     hexbin,
     Hmisc,
+    isoband,
     knitr,
     lattice,
     mapproj,
@@ -54,7 +55,7 @@ Suggests:
     rpart,
     sf (>= 0.7-3),
     svglite (>= 1.2.0.9001),
-    testthat (>= 0.11.0),
+    testthat (>= 2.1.0),
     vdiffr (>= 0.3.0)
 Enhances: sp
 License: GPL-2 | file LICENSE
@@ -190,6 +191,7 @@ Collate:
     'scale-continuous.r'
     'scale-date.r'
     'scale-discrete-.r'
+    'scale-expansion.r'
     'scale-gradient.r'
     'scale-grey.r'
     'scale-hue.r'
@@ -199,6 +201,7 @@ Collate:
     'scale-shape.r'
     'scale-size.r'
     'scale-type.R'
+    'scale-view.r'
     'scale-viridis.r'
     'scales-.r'
     'stat-bin.r'

NAMESPACE

@@ -49,6 +49,7 @@ S3method(ggplot_add,Coord)
 S3method(ggplot_add,Facet)
 S3method(ggplot_add,Layer)
 S3method(ggplot_add,Scale)
+S3method(ggplot_add,by)
 S3method(ggplot_add,data.frame)
 S3method(ggplot_add,default)
 S3method(ggplot_add,guides)
@@ -204,6 +205,7 @@ export(StatBindot)
 export(StatBinhex)
 export(StatBoxplot)
 export(StatContour)
+export(StatContourFilled)
 export(StatCount)
 export(StatDensity)
 export(StatDensity2d)
@@ -290,6 +292,7 @@ export(ensym)
 export(ensyms)
 export(expand_limits)
 export(expand_scale)
+export(expansion)
 export(expr)
 export(facet_grid)
 export(facet_null)
@@ -304,6 +307,7 @@ export(geom_blank)
 export(geom_boxplot)
 export(geom_col)
 export(geom_contour)
+export(geom_contour_filled)
 export(geom_count)
 export(geom_crossbar)
 export(geom_curve)
@@ -518,6 +522,7 @@ export(stat_bin_hex)
 export(stat_binhex)
 export(stat_boxplot)
 export(stat_contour)
+export(stat_contour_filled)
 export(stat_count)
 export(stat_density)
 export(stat_density2d)

NEWS.md

@@ -1,5 +1,60 @@
 # ggplot2 (development version)
 
+* stacking text when calculating the labels and the y axis with
+  `stat_summary()` now works (@ikosmidis, #2709)
+
+* Allowed reversing of discrete scales by re-writing `get_limits()` (@AnneLyng, #3115)
+
+* Added `stat_contour_filled()` and `geom_contour_filled()`, which compute 
+  and draw filled contours of gridded data (@paleolimbot, #3044).
+
+* `geom_contour()` and `stat_contour()` now use the isoband package
+  to compute contour lines. The `complete` parameter (which was undocumented
+  and has been unused for at least four years) was removed (@paleolimbot, #3044).
+
+* `stat_smooth()` user `REML` by default, if `method = "gam"` and
+  `gam`'s method is not specified (@ikosmidis, #2630).
+
+* Changed `theme_grey()` setting for legend key so that it creates no 
+  border (`NA`) rather than drawing a white one. (@annennenne, #3180)
+
+* Added function `ggplot_add.by()` for lists created with `by()` (#2734, @Maschette)
+
+* `ggdep()` was deprecated (@perezp44, #3382).
+
+* Added weight aesthetic option to `stat_density()` and made scaling of 
+  weights the default (@annennenne, #2902)
+
+* `expand_scale()` was deprecated in favour of `expansion()` for setting
+  the `expand` argument of `x` and `y` scales (@paleolimbot).
+
+* `coord_trans()` now draws second axes and accepts `xlim`, `ylim`,
+  and `expand` arguments to bring it up to feature parity with 
+  `coord_cartesian()`. The `xtrans` and `ytrans` arguments that were 
+  deprecated in version 1.0.1 in favour of `x` and `y` 
+  were removed (@paleolimbot, #2990).
+
+* `coord_trans()` now calculates breaks using the expanded range 
+  (previously these were calculated using the unexpanded range, 
+  which resulted in differences between plots made with `coord_trans()`
+  and those made with `coord_cartesian()`). The expansion for discrete axes 
+  in `coord_trans()` was also updated such that it behaves identically
+  to that in `coord_cartesian()` (@paleolimbot, #3338).
+
+* All `coord_*()` functions with `xlim` and `ylim` arguments now accept
+  vectors with `NA` as a placeholder for the minimum or maximum value
+  (e.g., `ylim = c(0, NA)` would zoom the y-axis from 0 to the 
+  maximum value observed in the data). This mimics the behaviour
+  of the `limits` argument in continuous scale functions
+  (@paleolimbot, #2907).
+
+* `geom_abline()`, `geom_hline()`, and `geom_vline()` now issue 
+  more informative warnings when supplied with set aesthetics
+  (i.e., `slope`, `intercept`, `yintercept`, and/or `xintercept`)
+  and mapped aesthetics (i.e., `data` and/or `mapping`).
+  
+* `stat_density2d()` can now take an `adjust` parameter to scale the default bandwidth. (#2860, @haleyjeppson)
+
 # ggplot2 3.2.1
 
 This is a patch release fixing a few regressions introduced in 3.2.0 as well as

R/aes.r

@@ -8,8 +8,8 @@ NULL
 #' [ggplot2()] and in individual layers.
 #'
 #' This function also standardises aesthetic names by converting `color` to `colour`
-#' (also in substrings, e.g. `point_color` to `point_colour`) and translating old style
-#' R names to ggplot names (eg. `pch` to `shape`, `cex` to `size`).
+#' (also in substrings, e.g., `point_color` to `point_colour`) and translating old style
+#' R names to ggplot names (e.g., `pch` to `shape` and `cex` to `size`).
 #'
 #' @section Quasiquotation:
 #'
@@ -22,9 +22,13 @@ NULL
 #' programming vignette](http://dplyr.tidyverse.org/articles/programming.html)
 #' to learn more about these techniques.
 #'
-#' @param x,y,... List of name value pairs giving aesthetics to map to
-#'   variables. The names for x and y aesthetics are typically omitted because
-#'   they are so common; all other aesthetics must be named.
+#' @param x,y,... List of name-value pairs in the form `aesthetic = variable`
+#'   describing which variables in the layer data should be mapped to which
+#'   aesthetics used by the paired geom/stat. The expression `variable` is
+#'   evaluated within the layer data, so there is no need to refer to
+#'   the original dataset (i.e., use `ggplot(df, aes(variable))`
+#'   instead of `ggplot(df, aes(df$variable))`). The names for x and y aesthetics
+#'   are typically omitted because they are so common; all other aesthetics must be named.
 #' @seealso [vars()] for another quoting function designed for
 #'   faceting specifications.
 #' @return A list with class `uneval`. Components of the list are either
@@ -334,3 +338,55 @@ mapped_aesthetics <- function(x) {
   is_null <- vapply(x, is.null, logical(1))
   names(x)[!is_null]
 }
+
+
+#' Check a mapping for discouraged usage
+#'
+#' Checks that `$` and `[[` are not used when the target *is* the data
+#'
+#' @param mapping A mapping created with [aes()]
+#' @param data The data to be mapped from
+#'
+#' @noRd
+warn_for_aes_extract_usage <- function(mapping, data) {
+  lapply(mapping, function(quosure) {
+    warn_for_aes_extract_usage_expr(get_expr(quosure), data, get_env(quosure))
+  })
+}
+
+warn_for_aes_extract_usage_expr <- function(x, data, env = emptyenv()) {
+  if (is_call(x, "[[") || is_call(x, "$")) {
+    if (extract_target_is_likely_data(x, data, env)) {
+      good_usage <- alternative_aes_extract_usage(x)
+      warning(
+        "Use of `", format(x), "` is discouraged. ",
+        "Use `", good_usage,  "` instead.",
+        call. = FALSE
+      )
+    }
+  } else if (is.call(x)) {
+    lapply(x, warn_for_aes_extract_usage_expr, data, env)
+  }
+}
+
+alternative_aes_extract_usage <- function(x) {
+  if (is_call(x, "[[")) {
+    good_call <- call2("[[", quote(.data), x[[3]])
+    format(good_call)
+  } else if (is_call(x, "$")) {
+    as.character(x[[3]])
+  } else {
+    stop("Don't know how to get alternative usage for `", format(x), "`", call. = FALSE)
+  }
+}
+
+extract_target_is_likely_data <- function(x, data, env) {
+  if (!is.name(x[[2]])) {
+    return(FALSE)
+  }
+
+  tryCatch({
+    data_eval <- eval_tidy(x[[2]], data, env)
+    identical(data_eval, data)
+  }, error = function(err) FALSE)
+}

R/axis-secondary.R

@@ -187,21 +187,49 @@ AxisSecondary <- ggproto("AxisSecondary", NULL,
 
     # patch for date and datetime scales just to maintain functionality
     # works only for linear secondary transforms that respect the time or date transform
-    if (scale$trans$name %in% c("date", "time")){
+    if (scale$trans$name %in% c("date", "time")) {
       temp_scale <- self$create_scale(new_range, trans = scale$trans)
       range_info <- temp_scale$break_info()
-      names(range_info) <- paste0("sec.", names(range_info))
-      return(range_info)
-    }
+      old_val_trans <- rescale(range_info$major, from = c(0, 1), to = range)
+      old_val_minor_trans <- rescale(range_info$minor, from = c(0, 1), to = range)
+    } else {
+      temp_scale <- self$create_scale(new_range)
+      range_info <- temp_scale$break_info()
 
-    temp_scale <- self$create_scale(new_range)
-    range_info <- temp_scale$break_info()
+      # Map the break values back to their correct position on the primary scale
+      old_val <- lapply(range_info$major_source, function(x) which.min(abs(full_range - x)))
+      old_val <- old_range[unlist(old_val)]
+      old_val_trans <- scale$trans$transform(old_val)
+
+      old_val_minor <- lapply(range_info$minor_source, function(x) which.min(abs(full_range - x)))
+      old_val_minor <- old_range[unlist(old_val_minor)]
+      old_val_minor_trans <- scale$trans$transform(old_val_minor)
+
+      # rescale values from 0 to 1
+      range_info$major[] <- round(
+        rescale(
+          scale$map(old_val_trans, range(old_val_trans)),
+          from = range
+        ),
+        digits = 3
+      )
+
+      range_info$minor[] <- round(
+        rescale(
+          scale$map(old_val_minor_trans, range(old_val_minor_trans)),
+          from = range
+        ),
+        digits = 3
+      )
+    }
 
-    # Map the break values back to their correct position on the primary scale
-    old_val <- lapply(range_info$major_source, function(x) which.min(abs(full_range - x)))
-    old_val <- old_range[unlist(old_val)]
-    old_val_trans <- scale$trans$transform(old_val)
-    range_info$major[] <- round(rescale(scale$map(old_val_trans, range(old_val_trans)), from = range), digits = 3)
+    # The _source values should be in (primary) scale_transformed space,
+    # so that the coord doesn't have to know about the secondary scale transformation
+    # when drawing the axis. The values in user space are useful for testing.
+    range_info$major_source_user <- range_info$major_source
+    range_info$minor_source_user <- range_info$minor_source
+    range_info$major_source[] <- old_val_trans
+    range_info$minor_source[] <- old_val_minor_trans
 
     names(range_info) <- paste0("sec.", names(range_info))
     range_info

R/bin.R

@@ -102,7 +102,7 @@ bin_breaks_bins <- function(x_range, bins = 30, center = NULL,
   if (bins < 1) {
     stop("Need at least one bin.", call. = FALSE)
   } else if (zero_range(x_range)) {
-    # 0.1 is the same width as the expansion `expand_default()` gives for 0-width data
+    # 0.1 is the same width as the expansion `default_expansion()` gives for 0-width data
     width <- 0.1
   } else if (bins == 1) {
     width <- diff(x_range)