initial commit

DESCRIPTION

@@ -1,6 +1,7 @@
 Package: gglogspline
 Type: Package
-Title: gglogspline title goes here otherwise CRAN checks fail
+Title: A 'ggplot2' Extension for Visualizing Density, Distribution, Hazard, or Survival 
+    Functions using the 'logspline' Package
 Version: 0.1.0
 Date: 2019-06-17
 Authors@R: c(
@@ -8,7 +9,8 @@ Authors@R: c(
            comment = c(ORCID = "0000-0001-5670-2640"))
   )
 Maintainer: Bob Rudis <bob@rud.is>
-Description: A good description goes here otherwise CRAN checks fail.
+Description: Methods are provided to plot a logspline density, distribution function, 
+    hazard function or survival function from a logspline density.
 URL: https://gitlab.com/hrbrmstr/gglogspline
 BugReports: https://gitlab.com/hrbrmstr/gglogspline/issues
 Encoding: UTF-8
@@ -19,7 +21,7 @@ Suggests:
 Depends:
     R (>= 3.2.0)
 Imports:
-    httr,
-    jsonlite
+    ggplot2,
+    logspline
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 6.1.1

NAMESPACE

@@ -1,4 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-import(httr)
-importFrom(jsonlite,fromJSON)
+export(StatLogspline)
+export(stat_logspline)
+import(ggplot2)
+import(logspline)

R/gglogspline-package.R

@@ -1,12 +1,12 @@
-#' ...
-#' 
-#' - URL: <https://gitlab.com/hrbrmstr/gglogspline>
-#' - BugReports: <https://gitlab.com/hrbrmstr/gglogspline/issues>
-#' 
+#' A 'ggplot2' Extension for Visualizing Density, Distribution, Hazard, or Survival
+#' Functions using the 'logspline' Package
+#'
+#' Methods are provided to plot a logspline density, distribution function,
+#' hazard function or survival function from a logspline density
+#'
 #' @md
 #' @name gglogspline
 #' @keywords internal
 #' @author Bob Rudis (bob@@rud.is)
-#' @import httr
-#' @importFrom jsonlite fromJSON
+#' @import ggplot2 logspline
 "_PACKAGE"

R/stat-logspline.R

@@ -0,0 +1,116 @@
+#' Base ggproto classes for gglogspline
+#'
+#' @section Computed variables:
+#'
+#' - `density` : the density estimate
+#' - `count`: computed counts (similar to [ggplots::stat_density()])
+#' - `probs`: distribution function
+#' - `survival`: survival function
+#' - `hazard` : hazard function
+#'
+#' By default the `y` aesthetic is mapped to `stat(density)`
+#'
+#' @rdname gglogspline-ggproto
+#' @export
+StatLogspline <- ggproto(
+
+  "StatLogspline", Stat,
+
+  compute_group = function(data, scales,
+                           n = 100, max_knots = 0, n_knots = 0,
+                           min_d = -1, error_action = 2) {
+
+    logspline(
+      data$x,
+      maxknots = max_knots,
+      nknots = n_knots,
+      mind = min_d,
+      error.action = error_action
+    ) -> lsp
+
+    # computed upper and lower bounds for simplicity
+
+    u1 <- qlogspline(0.01, lsp)
+    u2 <- qlogspline(0.99, lsp)
+
+    # we need these to compute the new x-axis values
+
+    u3 <- 1.1 * u1 - 0.1 * u2
+    u4 <- 1.1 * u2 - 0.1 * u1
+
+    # compute the new X-axis values and the log-density
+
+    xx <- (0:(n - 1))/(n - 1) * (u4 - u3) + u3
+    den <- dlogspline(xx, lsp)
+    prb <- plogspline(xx, lsp)
+
+    # our new data frame with an extra computed stat for the count
+
+    data.frame(
+      x = xx,
+      density = den,
+      probs = prb,
+      survival = 1 - prb,
+      hazard = den / (1 - prb),
+      count = den * nrow(data),
+      stringsAsFactors = FALSE
+    )
+
+  },
+
+  required_aes = c("x"), # we only accept one parameter
+
+  default_aes = aes(
+    y = stat(density) # by default we use the computed stat
+  )
+
+)
+
+#' Computes and draws...
+#'
+#' @inheritParams ggplot2::stat_density
+#' @param n numbe of points for the density estimation (larger == smoother)
+#' @param max_knots the maximum number of knots. The routine stops adding knots when
+#'        this number of knots is reached. The method has an automatic rule for selecting
+#'        maxknots if this parameter is not specified.
+#' @param n_knots forces the method to start with nknots knots. The method has an automatic
+#'        rule for selecting nknots if this parameter is not specified.
+#' @param min_d minimum distance, in order statistics, between knots.
+#' @param error_action see `error.action` in [logspline::plot.logspline()]
+#' @export
+#' @examples
+#' library(ggplot2)
+#'
+#' set.seed(1)
+#' data.frame(
+#'   val = rnorm(100)
+#' ) -> xdf
+#'
+#' ggplot(xdf) + stat_logspline(aes(val))
+stat_logspline <- function(mapping = NULL, data = NULL, geom = "area",
+                           position = "identity", na.rm = FALSE, show.legend = NA,
+                           inherit.aes = TRUE,
+                           # our custom params
+                           n = 100, max_knots = 0, n_knots = 0, min_d = -1, error_action = 2,
+                           ...) {
+
+  layer(
+    stat = StatLogspline,
+    data = data,
+    mapping = mapping,
+    geom = geom,
+    position = position,
+    show.legend = show.legend,
+    inherit.aes = inherit.aes,
+    params = list(
+      na.rm = na.rm,
+      # pass on our fancy custom params
+      n = n,
+      max_knots = max_knots,
+      n_knots = n_knots,
+      error_action = error_action,
+      ...
+    )
+  )
+
+}

README.Rmd

@@ -4,7 +4,7 @@ editor_options:
   chunk_output_type: inline
 ---
 ```{r pkg-knitr-opts, include=FALSE}
-knitr:: sopts_chunk$set(
+knitr::opts_chunk$set(
   collapse = TRUE, fig.retina = 2, message = FALSE, warning = FALSE
 )
 options(width=120)
@@ -16,8 +16,12 @@ options(width=120)
 
 # gglogspline
 
+A 'ggplot2' Extension for Visualizing Density, Distribution, Hazard, or Survival Functions using the 'logspline' Package
+
 ## Description
 
+Methods are provided to plot a logspline density, distribution function, hazard function or survival function from a logspline density
+
 ## What's Inside The Tin
 
 The following functions are implemented:
@@ -40,12 +44,39 @@ devtools::install_github("hrbrmstr/gglogspline")
 
 ```{r lib-ex}
 library(gglogspline)
+library(ggplot2)
 
 # current version
 packageVersion("gglogspline")
 
 ```
 
+```{r}
+set.seed(1)
+data.frame(
+  val = rnorm(100)
+) -> xdf
+
+ggplot(xdf) + 
+  stat_logspline(aes(val))
+
+ggplot(xdf) + 
+  stat_logspline(aes(val, y = stat(count))) +
+  labs(title = "logspline (count)")
+
+ggplot(xdf) +
+  stat_logspline(aes(val, y = stat(probs))) +
+  labs(title = "logspline (probability function)")
+
+ggplot(xdf) +
+  stat_logspline(aes(val, y = stat(survival))) +
+  labs(title = "logspline (survival function)")
+
+ggplot(xdf) +
+  stat_logspline(aes(val, y = stat(hazard))) +
+  labs(title = "logspline (hazard function)")
+```
+
 ## gglogspline Metrics
 
 ```{r cloc, echo=FALSE}

README.md

@@ -1,2 +1,106 @@
+
+[![Travis-CI Build
+Status](https://travis-ci.org/hrbrmstr/gglogspline.svg?branch=master)](https://travis-ci.org/hrbrmstr/gglogspline)
+[![Coverage
+Status](https://codecov.io/gh/hrbrmstr/gglogspline/branch/master/graph/badge.svg)](https://codecov.io/gh/hrbrmstr/gglogspline)
+[![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/gglogspline)](https://cran.r-project.org/package=gglogspline)
+
 # gglogspline
 
+A ‘ggplot2’ Extension for Visualizing Density, Distribution, Hazard, or
+Survival Functions using the ‘logspline’ Package
+
+## Description
+
+Methods are provided to plot a logspline density, distribution function,
+hazard function or survival function from a logspline density
+
+## What’s Inside The Tin
+
+The following functions are implemented:
+
+## Installation
+
+``` r
+devtools::install_git("https://git.sr.ht/~hrbrmstr/gglogspline.git")
+# or
+devtools::install_git("https://git.rud.is/hrbrmstr/gglogspline.git")
+# or
+devtools::install_gitlab("hrbrmstr/gglogspline")
+# or
+devtools::install_bitbucket("hrbrmstr/gglogspline")
+# or
+devtools::install_github("hrbrmstr/gglogspline")
+```
+
+## Usage
+
+``` r
+library(gglogspline)
+library(ggplot2)
+
+# current version
+packageVersion("gglogspline")
+## [1] '0.1.0'
+```
+
+``` r
+set.seed(1)
+data.frame(
+  val = rnorm(100)
+) -> xdf
+
+ggplot(xdf) + 
+  stat_logspline(aes(val))
+```
+
+<img src="README_files/figure-gfm/unnamed-chunk-1-1.png" width="672" />
+
+``` r
+
+ggplot(xdf) + 
+  stat_logspline(aes(val, y = stat(count))) +
+  labs(title = "logspline (count)")
+```
+
+<img src="README_files/figure-gfm/unnamed-chunk-1-2.png" width="672" />
+
+``` r
+
+ggplot(xdf) +
+  stat_logspline(aes(val, y = stat(probs))) +
+  labs(title = "logspline (probability function)")
+```
+
+<img src="README_files/figure-gfm/unnamed-chunk-1-3.png" width="672" />
+
+``` r
+
+ggplot(xdf) +
+  stat_logspline(aes(val, y = stat(survival))) +
+  labs(title = "logspline (survival function)")
+```
+
+<img src="README_files/figure-gfm/unnamed-chunk-1-4.png" width="672" />
+
+``` r
+
+ggplot(xdf) +
+  stat_logspline(aes(val, y = stat(hazard))) +
+  labs(title = "logspline (hazard function)")
+```
+
+<img src="README_files/figure-gfm/unnamed-chunk-1-5.png" width="672" />
+
+## gglogspline Metrics
+
+| Lang | \# Files | (%) | LoC |  (%) | Blank lines |  (%) | \# Lines | (%) |
+| :--- | -------: | --: | --: | ---: | ----------: | ---: | -------: | --: |
+| R    |        4 | 0.8 |  63 | 0.67 |          20 | 0.47 |       53 | 0.6 |
+| Rmd  |        1 | 0.2 |  31 | 0.33 |          23 | 0.53 |       35 | 0.4 |
+
+## 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.

man/gglogspline-ggproto.Rd

@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/stat-logspline.R
+\docType{data}
+\name{StatLogspline}
+\alias{StatLogspline}
+\title{Base ggproto classes for gglogspline}
+\format{An object of class \code{StatLogspline} (inherits from \code{Stat}, \code{ggproto}, \code{gg}) of length 4.}
+\usage{
+StatLogspline
+}
+\description{
+Base ggproto classes for gglogspline
+}
+\section{Computed variables}{
+
+\itemize{
+\item \code{density} : the density estimate
+\item \code{count}: computed counts (similar to \code{\link[ggplots:stat_density]{ggplots::stat_density()}})
+\item \code{probs}: distribution function
+\item \code{survival}: survival function
+\item \code{hazard} : hazard function
+}
+
+By default the \code{y} aesthetic is mapped to \code{stat(density)}
+}
+
+\keyword{datasets}

man/gglogspline.Rd

@@ -4,12 +4,11 @@
 \name{gglogspline}
 \alias{gglogspline}
 \alias{gglogspline-package}
-\title{...}
+\title{A 'ggplot2' Extension for Visualizing Density, Distribution, Hazard, or Survival
+Functions using the 'logspline' Package}
 \description{
-\itemize{
-\item URL: \url{https://gitlab.com/hrbrmstr/gglogspline}
-\item BugReports: \url{https://gitlab.com/hrbrmstr/gglogspline/issues}
-}
+Methods are provided to plot a logspline density, distribution function,
+hazard function or survival function from a logspline density
 }
 \seealso{
 Useful links:

man/stat_logspline.Rd

@@ -0,0 +1,83 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/stat-logspline.R
+\name{stat_logspline}
+\alias{stat_logspline}
+\title{Computes and draws...}
+\usage{
+stat_logspline(mapping = NULL, data = NULL, geom = "area",
+  position = "identity", na.rm = FALSE, show.legend = NA,
+  inherit.aes = TRUE, n = 100, max_knots = 0, n_knots = 0,
+  min_d = -1, error_action = 2, ...)
+}
+\arguments{
+\item{mapping}{Set of aesthetic mappings created by \code{\link[=aes]{aes()}} or
+\code{\link[=aes_]{aes_()}}. If specified and \code{inherit.aes = TRUE} (the
+default), it is combined with the default mapping at the top level of the
+plot. You must supply \code{mapping} if there is no plot mapping.}
+
+\item{data}{The data to be displayed in this layer. There are three
+options:
+
+If \code{NULL}, the default, the data is inherited from the plot
+data as specified in the call to \code{\link[=ggplot]{ggplot()}}.
+
+A \code{data.frame}, or other object, will override the plot
+data. All objects will be fortified to produce a data frame. See
+\code{\link[=fortify]{fortify()}} for which variables will be created.
+
+A \code{function} will be called with a single argument,
+the plot data. The return value must be a \code{data.frame}, and
+will be used as the layer data. A \code{function} can be created
+from a \code{formula} (e.g. \code{~ head(.x, 10)}).}
+
+\item{geom}{Use to override the default connection between
+\code{geom_density} and \code{stat_density}.}
+
+\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, missing values are removed with
+a warning. If \code{TRUE}, missing values are silently removed.}
+
+\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.
+It can also be a named logical vector to finely select the aesthetics to
+display.}
+
+\item{inherit.aes}{If \code{FALSE}, overrides the default aesthetics,
+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]{borders()}}.}
+
+\item{n}{numbe of points for the density estimation (larger == smoother)}
+
+\item{max_knots}{the maximum number of knots. The routine stops adding knots when
+this number of knots is reached. The method has an automatic rule for selecting
+maxknots if this parameter is not specified.}
+
+\item{n_knots}{forces the method to start with nknots knots. The method has an automatic
+rule for selecting nknots if this parameter is not specified.}
+
+\item{min_d}{minimum distance, in order statistics, between knots.}
+
+\item{error_action}{see \code{error.action} in \code{\link[logspline:plot.logspline]{logspline::plot.logspline()}}}
+
+\item{...}{Other arguments passed on to \code{\link[=layer]{layer()}}. These are
+often aesthetics, used to set an aesthetic to a fixed value, like
+\code{colour = "red"} or \code{size = 3}. They may also be parameters
+to the paired geom/stat.}
+}
+\description{
+Computes and draws...
+}
+\examples{
+library(ggplot2)
+
+set.seed(1)
+data.frame(
+  val = rnorm(100)
+) -> xdf
+
+ggplot(xdf) + stat_logspline(aes(val))
+}