pre-CRAN submission testing

.Rbuildignore

@@ -6,3 +6,4 @@
 ^CONDUCT\.md$
 ^README\.md$
 ^README_figs
+^README\.html$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ggalt
 Title: Alternate/Extra 'Geoms', 'Stats' and 'Coords' for 'ggplot2'
-Version: 0.0.4.9000
+Version: 0.1.0.9000
 Authors@R: c(person("Bob", "Rudis", email = "bob@rudis.net", role = c("aut", "cre")))
 Description: A package containing additional/alternate 'geoms', 'coords' and
     'stats' for use with the revamped (late 2015) version of ggplot2.
@@ -13,14 +13,17 @@ Suggests:
     testthat,
     gridExtra
 Encoding: UTF-8
+Enhances: ggplot2
 Imports:
     graphics,
     grDevices,
     dplyr,
+    RColorBrewer,
     KernSmooth,
     proj4,
     scales,
     grid,
     gtable,
-    ash
-RoxygenNote: 5.0.0
+    ash,
+    MASS
+RoxygenNote: 5.0.1

NAMESPACE

@@ -28,6 +28,7 @@ import(ggplot2)
 import(grDevices)
 import(graphics)
 import(proj4)
+importFrom(RColorBrewer,brewer.pal)
 importFrom(grid,gList)
 importFrom(grid,gTree)
 importFrom(grid,grid.draw)

R/coord_proj.r

@@ -2,10 +2,11 @@
 #'
 #' The representation of a portion of the earth, which is approximately
 #' spherical, onto a flat 2D plane requires a projection. This is what
-#' \code{coord_proj} does, using the \link[proj4]{project()} function from
+#' \code{coord_proj} does, using the \code{proj4::project()} function from
 #' the \code{proj4} package.
 #'
-#' @param proj projection definition
+#' @param proj projection definition. If left \code{NULL} will default to
+#'        a Robinson projection
 #' @param inverse	if \code{TRUE} inverse projection is performed (from a
 #'        cartographic projection into lat/long), otherwise projects from
 #'        lat/long into a cartographic projection.
@@ -20,10 +21,15 @@
 #' @param xlim manually specific x limits (in degrees of longitude)
 #' @param ylim manually specific y limits (in degrees of latitude)
 #' @export
-coord_proj <- function(proj="+proj=robin +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs",
-                       inverse = FALSE, degrees = TRUE,
+coord_proj <- function(proj=NULL, inverse = FALSE, degrees = TRUE,
                        ellps.default="sphere", xlim = NULL, ylim = NULL) {
 
+  if (is.null(proj)) {
+    proj <- paste0(c("+proj=robin +lon_0=0 +x_0=0 +y_0=0",
+                     "+ellps=WGS84 +datum=WGS84 +units=m +no_defs"),
+                   collapse=" ")
+  }
+
   ggproto(NULL, CoordProj,
     proj = proj,
     inverse = inverse,
@@ -35,6 +41,11 @@ coord_proj <- function(proj="+proj=robin +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +da
 
 }
 
+#' Geom Proto
+#' @rdname ggalt-ggproto
+#' @format NULL
+#' @usage NULL
+#' @keywords internal
 #' @export
 CoordProj <- ggproto("CoordProj", Coord,
 

R/geom_ash.r

@@ -79,6 +79,11 @@ stat_ash <- function(mapping = NULL, data = NULL, geom = "area",
 
 }
 
+#' Geom Proto
+#' @rdname ggalt-ggproto
+#' @format NULL
+#' @usage NULL
+#' @keywords internal
 #' @export
 StatAsh <- ggproto("StatAsh", Stat,
 

R/geom_bkde.r

@@ -42,9 +42,11 @@ geom_bkde <- function(mapping = NULL, data = NULL, stat = "bkde",
   )
 }
 
+#' Geom Proto
 #' @rdname ggalt-ggproto
 #' @format NULL
 #' @usage NULL
+#' @keywords internal
 #' @export
 GeomBkde <- ggproto("GeomBkde", GeomArea,
   default_aes = aes(colour = NA, fill = "gray20", size = 0.5,

R/geom_bkde2d.r

@@ -55,9 +55,11 @@ geom_bkde2d <- function(mapping = NULL, data = NULL, stat = "bkde2d",
 }
 
 
+#' Geom Proto
 #' @rdname ggalt-ggproto
 #' @format NULL
 #' @usage NULL
+#' @keywords internal
 #' @export
 GeomBkde2d <- ggproto("GeomBkde2d", GeomPath,
   default_aes = aes(colour = "#3366FF", size = 0.5, linetype = 1, alpha = NA)
@@ -73,9 +75,10 @@ GeomBkde2d <- ggproto("GeomBkde2d", GeomPath,
 #'        \code{\link[KernSmooth]{bkde2D}} for details. If \code{NULL},
 #'        it will be computed for you but will most likely not yield optimal
 #'        results. see \code{\link[KernSmooth]{bkde2D}} for details
-#' @param gridsize vector containing the number of equally spaced points in each
+#' @param grid_size vector containing the number of equally spaced points in each
 #'        direction over which the density is to be estimated. see
 #'        \code{\link[KernSmooth]{bkde2D}} for details
+#' @param geom default geom to use with this stat
 #' @param range.x	 a list containing two vectors, where each vector contains the
 #'        minimum and maximum values of x at which to compute the estimate for
 #'        each direction. see \code{\link[KernSmooth]{bkde2D}} for details

R/geom_xspline.r

@@ -127,17 +127,15 @@ geom_xspline <- function(mapping = NULL, data = NULL, stat = "xspline",
   )
 }
 
-#' GeomXspline
+#' Geom Proto
 #' @rdname ggalt-ggproto
 #' @format NULL
 #' @usage NULL
+#' @keywords internal
 #' @export
 GeomXspline <- ggproto("GeomXspline", GeomLine,
-
   required_aes = c("x", "y"),
-
   default_aes = aes(colour = "black", size = 0.5, linetype = 1, alpha = NA)
-
 )
 
 #' @export

R/ggalt-package.r

@@ -1,7 +1,6 @@
 #' Extra Geoms, Stats and Coords for 'ggplot2'
 #'
-#' A package containing additional geoms, coords and stats for the revamped
-#' (late 2015) version of ggplot2.
+#' A package containing additional geoms, coords and stats for the ggplot2 2.0+
 #'
 #' @name ggalt
 #' @docType package
@@ -11,4 +10,5 @@
 #' @importFrom grid grobName grobTree unit.c grobHeight grobWidth viewport
 #'                  grid.draw grobX grobY gTree gList
 #' @importFrom gtable gtable_col gtable_height gtable_width gtable_row gtable_col
+#' @importFrom RColorBrewer brewer.pal
 NULL

README.Rmd

@@ -1,5 +1,7 @@
 ---
 output:
+  html_document:
+    keep_md: true
   md_document:
     variant: markdown_github
 ---
@@ -17,17 +19,13 @@ fig.retina = 2,
 
 `ggalt` : Alternate/Extra 'Geoms', 'Stats' and 'Coords' for 'ggplot2'
 
- A package containing additional/alternate 'geoms', 'coords' and 'stats' for use with the revamped (late 2015) version of ggplot2.
+ A package containing additional/alternate 'geoms', 'coords' and 'stats' for use with ggplot2 2.0+.
 
 The first three forays into this brave, new `ggplot2` world are _splines_! and being able to use the (much better) `KernSmooth::bkde` and `KernSmooth::bkde2D` for density plots and an initial port of the (still needing work) `coord_proj`.
 
-**NOTE**
-
-Until the new `ggplot2` version is on CRAN, you'll need to install it from github via `devtools::install_github("hrbrmstr/ggplot2")`. Locally, I have goth `ggalt` and my `ggplot2` in a "develment mode" install via `devtools::dev_mode()`. Since the new `ggplot2` breaks _many_ other packages (like `plotly`, CRAN `ggthemes`, `ggmap` and more), keeping it squirreled away in it's own area is a good idea until everyone catches up.
-    
 The following functions are implemented:
 
-- `coord_proj` : Like `coord_map` only better `:-)`
+- `coord_proj` : Like `coord_map` only better 😜
 - `geom_xspline` : Connect control points/observations with an X-spline
 - `stat_xspline` : Connect control points/observations with an X-spline
 - `geom_bkde` :	Display a smooth density estimate (uses `KernSmooth::bkde`)
@@ -38,6 +36,7 @@ The following functions are implemented:
 
 ### News
 
+- Version 0.1.0.9000 released - Tweaks for ggplot2 2.0 release
 - Version 0.0.4.9000 released - `stat_ash`
 - Version 0.0.3.9000 released - `coord_proj`! (requires my github copy of ggplot2 for now)
 - Version 0.0.2.9005 released - cleanup before blog post
@@ -48,7 +47,7 @@ The following functions are implemented:
 
 ```{r eval=FALSE}
 # you'll want to see the vignettes, trust me
-devtools::install_github("hadley/ggplot2", build_vignettes=TRUE)
+install.packages("ggplot2")
 devtools::install_github("hrbrmstr/ggalt")
 ```
 
@@ -139,7 +138,7 @@ set.seed(1492)
 dat <- data.frame(cond = factor(rep(c("A","B"), each=200)), 
                    rating = c(rnorm(200),rnorm(200, mean=.8)))
 
-ggplot(dat, aes(x=rating, color=cond)) + geom_bkde(alpha=0)
+ggplot(dat, aes(x=rating, color=cond)) + geom_bkde(fill="#00000000")
 
 ggplot(dat, aes(x=rating, fill=cond)) + geom_bkde(alpha=0.3)
 
@@ -154,9 +153,9 @@ grid.arrange(ggplot(dat, aes(x)) + stat_ash(),
 
 cols <- RColorBrewer::brewer.pal(3, "Dark2")
 ggplot(dat, aes(x)) + 
-  stat_ash(alpha=1/2, fill=cols[3]) + 
-  stat_bkde(alpha=1/2, fill=cols[2]) + 
-  stat_density(alpha=1/2, fill=cols[1]) + 
+  stat_ash(alpha=1/3, fill=cols[3]) + 
+  stat_bkde(alpha=1/3, fill=cols[2]) + 
+  stat_density(alpha=1/3, fill=cols[1]) + 
   geom_rug() +
   labs(x=NULL, y="density/estimate") +
   scale_x_continuous(expand=c(0,0)) +
@@ -168,15 +167,15 @@ ggplot(dat, aes(x)) +
 ### Alternate 2D density plots
 
 ```{r bkde2d}
-geyser_dat <- data.frame(x=geyser$duration, y=geyser$waiting)
-
-ggplot(geyser_dat, aes(x, y)) +
+m <- ggplot(faithful, aes(x = eruptions, y = waiting)) +
        geom_point() +
-  geom_bkde2d(bandwidth=c(0.7, 7))
+       xlim(0.5, 6) +
+       ylim(40, 110)
+
+m + geom_bkde2d(bandwidth=c(0.5, 4))
+
+m + stat_bkde2d(bandwidth=c(0.5, 4), aes(fill = ..level..), geom = "polygon")
 
-ggplot(geyser_dat, aes(x, y)) +
-  geom_point() +
-  stat_bkde2d(bandwidth=c(0.7, 7))
 ```
 
 ### `coord_proj` LIVES! (still needs work)
@@ -193,17 +192,6 @@ gg <- gg + coord_proj("+proj=wintri")
 gg
 ```
 
-### Test Results
-
-```{r}
-library(ggalt)
-library(testthat)
-
-date()
-
-test_dir("tests/")
-```
-
 ### Code of Conduct
 
 Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). 

README.md

@@ -1,17 +1,17 @@
+
 <!-- README.md is generated from README.Rmd. Please edit that file -->
-`ggalt` : Alternate/Extra 'Geoms', 'Stats' and 'Coords' for 'ggplot2'
 
-A package containing additional/alternate 'geoms', 'coords' and 'stats' for use with the revamped (late 2015) version of ggplot2.
 
-The first three forays into this brave, new `ggplot2` world are *splines*! and being able to use the (much better) `KernSmooth::bkde` and `KernSmooth::bkde2D` for density plots and an initial port of the (still needing work) `coord_proj`.
 
-**NOTE**
+`ggalt` : Alternate/Extra 'Geoms', 'Stats' and 'Coords' for 'ggplot2'
+
+ A package containing additional/alternate 'geoms', 'coords' and 'stats' for use with ggplot2 2.0+.
 
-Until the new `ggplot2` version is on CRAN, you'll need to install it from github via `devtools::install_github("hrbrmstr/ggplot2")`. Locally, I have goth `ggalt` and my `ggplot2` in a "develment mode" install via `devtools::dev_mode()`. Since the new `ggplot2` breaks *many* other packages (like `plotly`, CRAN `ggthemes`, `ggmap` and more), keeping it squirreled away in it's own area is a good idea until everyone catches up.
+The first three forays into this brave, new `ggplot2` world are _splines_! and being able to use the (much better) `KernSmooth::bkde` and `KernSmooth::bkde2D` for density plots and an initial port of the (still needing work) `coord_proj`.
 
 The following functions are implemented:
 
--   `coord_proj` : Like `coord_map` only better `:-)`
+- `coord_proj` : Like `coord_map` only better 😜
 - `geom_xspline` : Connect control points/observations with an X-spline
 - `stat_xspline` : Connect control points/observations with an X-spline
 - `geom_bkde` :	Display a smooth density estimate (uses `KernSmooth::bkde`)
@@ -22,6 +22,7 @@ The following functions are implemented:
 
 ### News
 
+- Version 0.1.0.9000 released - Tweaks for ggplot2 2.0 release
 - Version 0.0.4.9000 released - `stat_ash`
 - Version 0.0.3.9000 released - `coord_proj`! (requires my github copy of ggplot2 for now)
 - Version 0.0.2.9005 released - cleanup before blog post
@@ -30,14 +31,18 @@ The following functions are implemented:
 
 ### Installation
 
+
 ```r
 # you'll want to see the vignettes, trust me
-devtools::install_github("hadley/ggplot2", build_vignettes=TRUE)
+install.packages("ggplot2")
 devtools::install_github("hrbrmstr/ggalt")
 ```
 
+
+
 ### Usage
 
+
 ```r
 library(ggplot2)
 library(gridExtra)
@@ -45,7 +50,7 @@ library(ggalt)
 
 # current verison
 packageVersion("ggalt")
-#> [1] '0.0.4.9000'
+#> [1] '0.1.0.9000'
 
 set.seed(1492)
 dat <- data.frame(x=c(1:10, 1:10, 1:10),
@@ -56,6 +61,7 @@ dat <- data.frame(x=c(1:10, 1:10, 1:10),
 
 ### Splines!
 
+
 ```r
 ggplot(dat, aes(x, y, group=group, color=group)) +
   geom_point() +
@@ -136,6 +142,7 @@ ggplot(dat, aes(x, y, group=group, color=factor(group))) +
 
 #### Alternate (better) density plots
 
+
 ```r
 # bkde
 
@@ -179,7 +186,7 @@ set.seed(1492)
 dat <- data.frame(cond = factor(rep(c("A","B"), each=200)), 
                    rating = c(rnorm(200),rnorm(200, mean=.8)))
 
-ggplot(dat, aes(x=rating, color=cond)) + geom_bkde(alpha=0)
+ggplot(dat, aes(x=rating, color=cond)) + geom_bkde(fill="#00000000")
 #> Bandwidth not specified. Using '0.36', via KernSmooth::dpik.
 #> Bandwidth not specified. Using '0.31', via KernSmooth::dpik.
 ```
@@ -215,9 +222,9 @@ grid.arrange(ggplot(dat, aes(x)) + stat_ash(),
 
 cols <- RColorBrewer::brewer.pal(3, "Dark2")
 ggplot(dat, aes(x)) + 
-  stat_ash(alpha=1/2, fill=cols[3]) + 
-  stat_bkde(alpha=1/2, fill=cols[2]) + 
-  stat_density(alpha=1/2, fill=cols[1]) + 
+  stat_ash(alpha=1/3, fill=cols[3]) + 
+  stat_bkde(alpha=1/3, fill=cols[2]) + 
+  stat_density(alpha=1/3, fill=cols[1]) + 
   geom_rug() +
   labs(x=NULL, y="density/estimate") +
   scale_x_continuous(expand=c(0,0)) +
@@ -232,27 +239,28 @@ ggplot(dat, aes(x)) +
 
 ### Alternate 2D density plots
 
-``` r
-geyser_dat <- data.frame(x=geyser$duration, y=geyser$waiting)
 
-ggplot(geyser_dat, aes(x, y)) +
+```r
+m <- ggplot(faithful, aes(x = eruptions, y = waiting)) +
        geom_point() +
-  geom_bkde2d(bandwidth=c(0.7, 7))
+       xlim(0.5, 6) +
+       ylim(40, 110)
+
+m + geom_bkde2d(bandwidth=c(0.5, 4))
 ```
 
 <img src="README_figs/README-bkde2d-1.png" title="" alt="" width="672" />
 
 ```r
 
-ggplot(geyser_dat, aes(x, y)) +
-  geom_point() +
-  stat_bkde2d(bandwidth=c(0.7, 7))
+m + stat_bkde2d(bandwidth=c(0.5, 4), aes(fill = ..level..), geom = "polygon")
 ```
 
 <img src="README_figs/README-bkde2d-2.png" title="" alt="" width="672" />
 
 ### `coord_proj` LIVES! (still needs work)
 
+
 ```r
 # devtools::install_github("hrbrmstr/ggplot2")
 world <- map_data("world")
@@ -271,20 +279,7 @@ gg
 
 <img src="README_figs/README-coord_proj-1.png" title="" alt="" width="672" />
 
-### Test Results
-
-``` r
-library(ggalt)
-library(testthat)
-
-date()
-#> [1] "Sat Oct 31 10:07:15 2015"
-
-test_dir("tests/")
-#> testthat results ========================================================================================================
-#> OK: 0 SKIPPED: 0 FAILED: 0
-```
-
 ### Code of Conduct
 
-Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.
+Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). 
+By participating in this project you agree to abide by its terms.

man/coord_proj.Rd

@@ -4,13 +4,12 @@
 \alias{coord_proj}
 \title{Like \code{coord_map} only better :-)}
 \usage{
-
-  coord_proj(proj = "+proj=robin +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs",
-  inverse = FALSE, degrees = TRUE, ellps.default = "sphere",
-  xlim = NULL, ylim = NULL)
+coord_proj(proj = NULL, inverse = FALSE, degrees = TRUE,
+  ellps.default = "sphere", xlim = NULL, ylim = NULL)
 }
 \arguments{
-\item{proj}{projection definition}
+\item{proj}{projection definition. If left \code{NULL} will default to
+a Robinson projection}
 
 \item{inverse}{if \code{TRUE} inverse projection is performed (from a
 cartographic projection into lat/long), otherwise projects from
@@ -33,7 +32,7 @@ directly).}
 \description{
 The representation of a portion of the earth, which is approximately
 spherical, onto a flat 2D plane requires a projection. This is what
-\code{coord_proj} does, using the \link[proj4]{project()} function from
+\code{coord_proj} does, using the \code{proj4::project()} function from
 the \code{proj4} package.
 }
 

man/geom_bkde2d.Rd

@@ -72,13 +72,15 @@ the default plot specification, e.g. \code{\link{borders}}.}
   \item Other arguments passed on to the stat.
   }}
 
-\item{truncate}{logical flag: if TRUE, data with x values outside the range
-specified by range.x are ignored. see \code{\link[KernSmooth]{bkde2D}}
-for details}
+\item{geom}{default geom to use with this stat}
 
-\item{gridsize}{vector containing the number of equally spaced points in each
+\item{grid_size}{vector containing the number of equally spaced points in each
 direction over which the density is to be estimated. see
 \code{\link[KernSmooth]{bkde2D}} for details}
+
+\item{truncate}{logical flag: if TRUE, data with x values outside the range
+specified by range.x are ignored. see \code{\link[KernSmooth]{bkde2D}}
+for details}
 }
 \description{
 Contours from a 2d density estimate.

man/ggalt-ggproto.Rd

@@ -1,16 +1,27 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/geom_bkde.r, R/geom_bkde2d.r, R/geom_xspline.r
+% Please edit documentation in R/coord_proj.r, R/geom_ash.r, R/geom_bkde.r, R/geom_bkde2d.r, R/geom_xspline.r
 \docType{data}
-\name{GeomBkde}
+\name{CoordProj}
+\alias{CoordProj}
 \alias{GeomBkde}
 \alias{GeomBkde2d}
 \alias{GeomXspline}
+\alias{StatAsh}
 \alias{StatBkde}
 \alias{StatBkde2d}
 \alias{StatXspline}
-\title{GeomXspline}
+\title{Geom Proto}
 \description{
-GeomXspline
+Geom Proto
+
+Geom Proto
+
+Geom Proto
+
+Geom Proto
+
+Geom Proto
 }
 \keyword{datasets}
+\keyword{internal}
 

man/ggalt.Rd

@@ -6,8 +6,7 @@
 \alias{ggalt-package}
 \title{Extra Geoms, Stats and Coords for 'ggplot2'}
 \description{
-A package containing additional geoms, coords and stats for the revamped
-(late 2015) version of ggplot2.
+A package containing additional geoms, coords and stats for the ggplot2 2.0+
 }
 \author{
 Bob Rudis (@hrbrmstr)