compiled with new na.rm policy in ggplot2

DESCRIPTION

@@ -1,12 +1,26 @@
 Package: ggalt
 Title: Alternate/Extra 'Geoms', 'Stats' and 'Coords' for 'ggplot2'
-Version: 0.0.3.9000
+Version: 0.0.4.9000
 Authors@R: c(person("Bob", "Rudis", email = "bob@rudis.net", role = c("aut", "cre")))
-Description: A package containing additional/alternate 'geoms', 'coords' and 'stats'
+Description: A package containing additional/alternate 'geoms', 'coords' and
-    for use with the revamped (late 2015) version of ggplot2.
+    'stats' for use with the revamped (late 2015) version of ggplot2.
-Depends: R (>= 3.0.0), ggplot2 (>= 1.0.1.9003)
+Depends:
+    R (>= 3.0.0),
+    ggplot2 (>= 1.0.1.9003)
 License: AGPL + file LICENSE
 LazyData: true
-Suggests: testthat, gridExtra
+Suggests:
+    testthat,
+    gridExtra
 Encoding: UTF-8
-Imports: graphics, grDevices, dplyr, KernSmooth, proj4, scales, grid, gtable, ash
+Imports:
+    graphics,
+    grDevices,
+    dplyr,
+    KernSmooth,
+    proj4,
+    scales,
+    grid,
+    gtable,
+    ash
+RoxygenNote: 5.0.0

NAMESPACE

@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.1.1): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 S3method(grid.draw,absoluteGrob)
 S3method(grobHeight,absoluteGrob)

R/geom_ash.r

@@ -57,7 +57,7 @@
 stat_ash <- function(mapping = NULL, data = NULL, geom = "area",
                      position = "stack",
                      ab = NULL, nbin = 50, m = 5, kopt = c(2, 2),
-                     show.legend = NA, inherit.aes = TRUE, ...) {
+                     na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, ...) {
 
   layer(
     data = data,
@@ -68,6 +68,7 @@ stat_ash <- function(mapping = NULL, data = NULL, geom = "area",
     show.legend = show.legend,
     inherit.aes = inherit.aes,
     params = list(
+      na.rm = na.rm,
       ab = ab,
       nbin = nbin,
       m = m,

R/geom_bkde.r

@@ -15,17 +15,16 @@
 #'   \item \code{linetype}
 #'   \item \code{size}
 #' }
-#'
+#' @inheritParams ggplot2::geom_point
 #' @param geom,stat Use to override the default connection between
 #'   \code{geom_bkde} and \code{stat_bkde}.
 #' @seealso See \code{\link{geom_histogram}}, \code{\link{geom_freqpoly}} for
 #'   other methods of displaying continuous distribution.
 #'   See \code{\link{geom_violin}} for a compact density display.
-#' @inheritParams ggplot2::geom_point
 #' @export
 geom_bkde <- function(mapping = NULL, data = NULL, stat = "bkde",
                       position = "identity", bandwidth=NULL, range.x=NULL,
-                      show.legend = NA, inherit.aes = TRUE,
+                      na.rm = FALSE, show.legend = NA, inherit.aes = TRUE,
                       ...) {
 
   layer(
@@ -38,6 +37,7 @@ geom_bkde <- function(mapping = NULL, data = NULL, stat = "bkde",
     inherit.aes = inherit.aes,
     params = list(bandwidth=bandwidth,
                   range.x=range.x,
+                  na.rm=na.rm,
                   ...)
   )
 }
@@ -93,7 +93,7 @@ GeomBkde <- ggproto("GeomBkde", GeomArea,
 stat_bkde <- function(mapping = NULL, data = NULL, geom = "area",
                       position = "stack", kernel="normal", canonical=FALSE,
                       bandwidth = NULL, gridsize=410, range.x=NULL,
-                      truncate=TRUE, show.legend = NA, inherit.aes = TRUE,
+                      truncate=TRUE, na.rm=FALSE, show.legend = NA, inherit.aes = TRUE,
                       ...) {
 
   layer(
@@ -111,6 +111,7 @@ stat_bkde <- function(mapping = NULL, data = NULL, geom = "area",
       gridsize=gridsize,
       range.x=range.x,
       truncate=truncate,
+      na.rm=na.rm,
       ...
     )
   )
@@ -129,7 +130,7 @@ StatBkde <- ggproto("StatBkde", Stat,
 
   compute_group = function(data, scales, kernel="normal", canonical=FALSE,
                            bandwidth=NULL, gridsize=410, range.x=NULL,
-                           truncate=TRUE) {
+                           truncate=TRUE, na.rm = TRUE) {
 
     # KernSmooth::dpik uses a generated normal distribution as part of it's
     # operation but doesn't do this seed save/create/restore. When bandwidth
@@ -152,14 +153,14 @@ StatBkde <- ggproto("StatBkde", Stat,
 
     compute_bkde(data$x, kernel=kernel, canonical=canonical,
                     bandwidth=bandwidth, gridsize=gridsize, range.x=range.x,
-                    truncate=truncate)
+                    truncate=truncate, na.rm)
 
   }
 
 )
 
 compute_bkde <- function(x, kernel="normal", canonical=FALSE,
-                        bandwidth, gridsize=410, range.x, truncate=TRUE) {
+                        bandwidth, gridsize=410, range.x, truncate=TRUE, na.rm=TRUE) {
 
   n <- length(x)
 
@@ -170,7 +171,7 @@ compute_bkde <- function(x, kernel="normal", canonical=FALSE,
   data.frame(
     x = dens$x,
     density = dens$y,
-    scaled =  dens$y / max(dens$y, na.rm = TRUE),
+    scaled =  dens$y / max(dens$y, na.rm = na.rm),
     count =   dens$y * n,
     n = n
   )

R/geom_bkde2d.r

@@ -32,7 +32,7 @@ geom_bkde2d <- function(mapping = NULL, data = NULL, stat = "bkde2d",
                            position = "identity",  bandwidth=NULL, range.x=NULL,
                            lineend = "butt", contour=TRUE,
                            linejoin = "round", linemitre = 1,
-                           show.legend = NA,
+                           na.rm = FALSE, show.legend = NA,
                            inherit.aes = TRUE, ...) {
   layer(
     data = data,
@@ -48,6 +48,7 @@ geom_bkde2d <- function(mapping = NULL, data = NULL, stat = "bkde2d",
       linemitre = linemitre,
       bandwidth = bandwidth,
       range.x = range.x,
+      na.rm = na.rm,
       ...
     )
   )
@@ -92,7 +93,7 @@ GeomBkde2d <- ggproto("GeomBkde2d", GeomPath,
 stat_bkde2d <- function(mapping = NULL, data = NULL, geom = "density2d",
                            position = "identity", contour = TRUE,
                            bandwidth=NULL, grid_size=c(51, 51), range.x=NULL,
-                           truncate=TRUE, show.legend = NA,
+                           truncate=TRUE, na.rm = FALSE, show.legend = NA,
                            inherit.aes = TRUE, ...) {
   layer(
     data = data,
@@ -108,6 +109,7 @@ stat_bkde2d <- function(mapping = NULL, data = NULL, geom = "density2d",
       range.x = range.x,
       truncate = truncate,
       contour = contour,
+      na.rm = na.rm,
       ...
     )
   )

R/geom_xspline.r

@@ -108,8 +108,8 @@
 #'   geom_smooth(se=FALSE, linetype="dashed", size=0.5) +
 #'   geom_xspline(spline_shape=-1, size=0.5)
 geom_xspline <- function(mapping = NULL, data = NULL, stat = "xspline",
-                      position = "identity", show.legend = NA,
+                      position = "identity", na.rm = TRUE, show.legend = NA,
-                      inherit.aes = TRUE, na.rm = TRUE,
+                      inherit.aes = TRUE,
                       spline_shape=-0.25, open=TRUE, rep_ends=TRUE, ...) {
   layer(
     geom = GeomXspline,
@@ -121,6 +121,7 @@ geom_xspline <- function(mapping = NULL, data = NULL, stat = "xspline",
     inherit.aes = inherit.aes,
     params = list(spline_shape=spline_shape,
                   open=open,
+                  na.rm = na.rm,
                   rep_ends=rep_ends,
                   ...)
   )
@@ -147,7 +148,7 @@ GeomXspline <- ggproto("GeomXspline", GeomLine,
 #'   \item{y}
 #' }
 stat_xspline <- function(mapping = NULL, data = NULL, geom = "line",
-                     position = "identity", show.legend = NA, inherit.aes = TRUE,
+                     position = "identity", na.rm = TRUE, show.legend = NA, inherit.aes = TRUE,
                      spline_shape=-0.25, open=TRUE, rep_ends=TRUE, ...) {
   layer(
     stat = StatXspline,
@@ -159,6 +160,7 @@ stat_xspline <- function(mapping = NULL, data = NULL, geom = "line",
     inherit.aes = inherit.aes,
     params = list(spline_shape=spline_shape,
                   open=open,
+                  na.rm = na.rm,
                   rep_ends=rep_ends,
                   ...
     )

README.Rmd

@@ -10,7 +10,7 @@ output:
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
-  fig.retina = 2,
+fig.retina = 2,
   fig.path = "README_figs/README-"
 )
 ```

README.md

@@ -45,7 +45,7 @@ library(ggalt)
 
 # current verison
 packageVersion("ggalt")
-#> [1] '0.0.3.9000'
+#> [1] '0.0.4.9000'
 
 set.seed(1492)
 dat <- data.frame(x=c(1:10, 1:10, 1:10),
@@ -256,6 +256,10 @@ ggplot(geyser_dat, aes(x, y)) +
 ``` r
 # devtools::install_github("hrbrmstr/ggplot2")
 world <- map_data("world")
+#> 
+#>  # ATTENTION: maps v3.0 has an updated 'world' map.        #
+#>  # Many country borders and names have changed since 1990. #
+#>  # Type '?world' or 'news(package="maps")'. See README_v3. #
 world <- world[world$region != "Antarctica",]
 
 gg <- ggplot()
@@ -274,13 +278,11 @@ library(ggalt)
 library(testthat)
 
 date()
-#> [1] "Sun Sep 13 07:33:03 2015"
+#> [1] "Sat Oct 31 10:07:15 2015"
 
 test_dir("tests/")
 #> testthat results ========================================================================================================
 #> OK: 0 SKIPPED: 0 FAILED: 0
-#> 
-#> DONE
 ```
 
 ### Code of Conduct

man/absoluteGrob.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/grob_absolute.r
 \name{absoluteGrob}
 \alias{absoluteGrob}

man/coord_proj.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/coord_proj.r
 \name{coord_proj}
 \alias{coord_proj}

man/geom_bkde.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/geom_bkde.r
 \name{geom_bkde}
 \alias{geom_bkde}
@@ -7,12 +7,12 @@
 \usage{
 geom_bkde(mapping = NULL, data = NULL, stat = "bkde",
   position = "identity", bandwidth = NULL, range.x = NULL,
-  show.legend = NA, inherit.aes = TRUE, ...)
+  na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, ...)
 
 stat_bkde(mapping = NULL, data = NULL, geom = "area",
   position = "stack", kernel = "normal", canonical = FALSE,
   bandwidth = NULL, gridsize = 410, range.x = NULL, truncate = TRUE,
-  show.legend = NA, inherit.aes = TRUE, ...)
+  na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, ...)
 }
 \arguments{
 \item{mapping}{Set of aesthetic mappings created by \code{\link{aes}} or
@@ -35,6 +35,9 @@ results.}
 \item{range.x}{vector containing the minimum and maximum values of x at which
 to compute the estimate. see \code{\link[KernSmooth]{bkde}} for details}
 
+\item{na.rm}{If \code{FALSE} (the default), removes missing values with
+a warning.  If \code{TRUE} silently removes missing values.}
+
 \item{show.legend}{logical. Should this layer be included in the legends?
 \code{NA}, the default, includes if any aesthetics are mapped.
 \code{FALSE} never includes, and \code{TRUE} always includes.}
@@ -55,7 +58,7 @@ the default plot specification, e.g. \code{\link{borders}}.}
   \item Other arguments passed on to the stat.
   }}
 
-\item{geom,stat}{Use to override the default connection between
+\item{geom, stat}{Use to override the default connection between
 \code{geom_bkde} and \code{stat_bkde}.}
 
 \item{kernel}{character string which determines the smoothing kernel. see

man/geom_bkde2d.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/geom_bkde2d.r
 \name{geom_bkde2d}
 \alias{geom_bkde2d}
@@ -8,11 +8,11 @@
 geom_bkde2d(mapping = NULL, data = NULL, stat = "bkde2d",
   position = "identity", bandwidth = NULL, range.x = NULL,
   lineend = "butt", contour = TRUE, linejoin = "round", linemitre = 1,
-  show.legend = NA, inherit.aes = TRUE, ...)
+  na.rm = FALSE, show.legend = NA, inherit.aes = TRUE, ...)
 
 stat_bkde2d(mapping = NULL, data = NULL, geom = "density2d",
   position = "identity", contour = TRUE, bandwidth = NULL,
-  grid_size = c(51, 51), range.x = NULL, truncate = TRUE,
+  grid_size = c(51, 51), range.x = NULL, truncate = TRUE, na.rm = FALSE,
   show.legend = NA, inherit.aes = TRUE, ...)
 }
 \arguments{
@@ -49,6 +49,9 @@ estimation}
 
 \item{linemitre}{Line mitre limit (number greater than 1)}
 
+\item{na.rm}{If \code{FALSE} (the default), removes missing values with
+a warning.  If \code{TRUE} silently removes missing values.}
+
 \item{show.legend}{logical. Should this layer be included in the legends?
 \code{NA}, the default, includes if any aesthetics are mapped.
 \code{FALSE} never includes, and \code{TRUE} always includes.}

man/geom_xspline.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/geom_xspline.r
 \name{geom_xspline}
 \alias{geom_xspline}
@@ -6,12 +6,14 @@
 \title{Connect control points/observations with an X-spline}
 \usage{
 geom_xspline(mapping = NULL, data = NULL, stat = "xspline",
-  position = "identity", show.legend = NA, inherit.aes = TRUE,
+  position = "identity", na.rm = TRUE, show.legend = NA,
-  na.rm = TRUE, spline_shape = -0.25, open = TRUE, rep_ends = TRUE, ...)
+  inherit.aes = TRUE, spline_shape = -0.25, open = TRUE,
+  rep_ends = TRUE, ...)
 
 stat_xspline(mapping = NULL, data = NULL, geom = "line",
-  position = "identity", show.legend = NA, inherit.aes = TRUE,
+  position = "identity", na.rm = TRUE, show.legend = NA,
-  spline_shape = -0.25, open = TRUE, rep_ends = TRUE, ...)
+  inherit.aes = TRUE, spline_shape = -0.25, open = TRUE,
+  rep_ends = TRUE, ...)
 }
 \arguments{
 \item{mapping}{Set of aesthetic mappings created by \code{\link{aes}} or
@@ -26,6 +28,9 @@ defined at the top level of the plot.}
 \item{position}{Position adjustment, either as a string, or the result of
 a call to a position adjustment function.}
 
+\item{na.rm}{If \code{FALSE} (the default), removes missing values with
+a warning.  If \code{TRUE} silently removes missing values.}
+
 \item{show.legend}{logical. Should this layer be included in the legends?
 \code{NA}, the default, includes if any aesthetics are mapped.
 \code{FALSE} never includes, and \code{TRUE} always includes.}
@@ -35,9 +40,6 @@ rather than combining with them. This is most useful for helper functions
 that define both data and aesthetics and shouldn't inherit behaviour from
 the default plot specification, e.g. \code{\link{borders}}.}
 
-\item{na.rm}{If \code{FALSE} (the default), removes missing values with
-a warning.  If \code{TRUE} silently removes missing values.}
-
 \item{spline_shape}{A numeric vector of values between -1 and 1, which
 control the shape of the spline relative to the control points.}
 
@@ -59,7 +61,7 @@ curve. Ignored for closed X-splines.}
   \item Other arguments passed on to the stat.
   }}
 
-\item{geom,stat}{Use to override the default connection between
+\item{geom, stat}{Use to override the default connection between
 \code{geom_xspline} and \code{stat_xspline}.}
 }
 \description{

man/ggalt-ggproto.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/geom_bkde.r, R/geom_bkde2d.r, R/geom_xspline.r
 \docType{data}
 \name{GeomBkde}

man/ggalt.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/ggalt-package.r
 \docType{package}
 \name{ggalt}

man/stat_ash.Rd

@@ -1,12 +1,12 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
+% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/geom_ash.r
 \name{stat_ash}
 \alias{stat_ash}
 \title{Compute and display a univariate averaged shifted histogram (polynomial kernel)}
 \usage{
 stat_ash(mapping = NULL, data = NULL, geom = "area", position = "stack",
-  ab = NULL, nbin = 50, m = 5, kopt = c(2, 2), show.legend = NA,
+  ab = NULL, nbin = 50, m = 5, kopt = c(2, 2), na.rm = FALSE,
-  inherit.aes = TRUE, ...)
+  show.legend = NA, inherit.aes = TRUE, ...)
 }
 \arguments{
 \item{mapping}{Set of aesthetic mappings created by \code{\link{aes}} or
@@ -35,6 +35,9 @@ interval.}
 to \emph{( 1 - abs(i/m)^kopt(1) )i^kopt(2)}; (2,2)=biweight (default);
  (0,0)=uniform; (1,0)=triangle; (2,1)=Epanechnikov; (2,3)=triweight.}
 
+\item{na.rm}{If \code{FALSE} (the default), removes missing values with
+a warning.  If \code{TRUE} silently removes missing values.}
+
 \item{show.legend}{logical. Should this layer be included in the legends?
 \code{NA}, the default, includes if any aesthetics are mapped.
 \code{FALSE} never includes, and \code{TRUE} always includes.}