Merge pull request #4 from tzerk/master

v0.1.0
R-Lum · Mar 31, 2015 · 94dfcd5 · 94dfcd5
2 parents 9c72638 + 1b59067
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,7 +1,7 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-LICENSE$
 README.md$
 ^.Rprofile$
 ^\.Rprofile$
-.Rprofile
+.Rprofile
+cran-comments.md$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,13 +1,19 @@
 Package: RLumShiny
 Type: Package
-Title: Shiny Applications for the R Package Luminescence
-Version: 0.1.0.9000
-Date: 2015-02-25
-Authors@R: c(person("Christoph", "Burow", role = c("aut", "cre"), email = "christoph.burow@uni-koeln.de")
+Title: 'Shiny' Applications for the R Package 'Luminescence'
+Version: 0.1.0
+Date: 2015-03-31
+Authors@R: c(
+    person("Christoph", "Burow", role = c("aut", "cre"), email = "christoph.burow@uni-koeln.de"),
+    person("Jan", "Odvarko", role = "cph", comment = "jscolor.js in www/jscolor"),
+    person(family = "AnalytixWare", role = "cph", comment = "ShinySky package" )
     )
-Author: Christoph Burow [aut, cre]
 Maintainer: Christoph Burow <christoph.burow@uni-koeln.de>
-Description: A collection of shiny applications for the R package Luminescence. These mainly, but not exclusively, include applications for plotting chronometric data from e.g. luminescence or radiocarbon dating. It further provides access to bootstraps tooltip and popover functionality as well as a binding to JSColor.
+Description: A collection of 'shiny' applications for the R package 'Luminescence'. 
+      These mainly, but not exclusively, include applications for plotting chronometric 
+      data from e.g. luminescence or radiocarbon dating. It further provides access to 
+      bootstraps tooltip and popover functionality and contains the 'jscolor.js' library
+      with a custom 'shiny' output binding.
 License: GPL-3
 Depends:
     R (>= 3.1.2)
@@ -24,4 +30,5 @@ Collate:
     'jscolor.R'
     'tooltip.R'
     'popover.R'
+    'RLumShiny.R'
     'zzz.R'
diff --git a/LICENSE b/LICENSE
diff --git a/LICENSE.note b/LICENSE.note
@@ -0,0 +1,8 @@
+The RLumShiny package as a whole is distributed under GPL-3 (GNU GENERAL PUBLIC
+LICENSE version 3).
+
+The RLumShiny package includes other open source software components. The following
+is a list of these components:
+
+- JSColor, https://github.com/odvarko/jscolor, LGPL License
+- ShinySky, https://github.com/AnalytixWare/ShinySky, MIT license (YEAR: 2015, COPYRIGHT HOLDER: AnalytixWare)
diff --git a/NAMESPACE b/NAMESPACE
@@ -4,4 +4,8 @@ export(app_RLum)
 export(jscolorInput)
 export(popover)
 export(tooltip)
+import(Luminescence)
+import(RCurl)
+import(digest)
+import(googleVis)
 import(shiny)
diff --git a/NEWS b/NEWS
@@ -1,26 +1,4 @@
-NEWS for the R Package ESR
-
-Changes in version 0.1.x (XXXXXXX XXth, 2015):
-
-  Preface:
-
-         • 
-
-  New functions:
-
-         • 
-
-  New example data sets:
-
-         • 
-
-  Bugfixes and changes:
-
-         • 
-
-             • 
-
-  Internals:
-
-         • 
+RLumShiny 0.1.0 (Release date: 2015-03-31)
+==============
 
+* Initial release
diff --git a/R/RLumShiny.R b/R/RLumShiny.R
@@ -0,0 +1,21 @@
+#' Shiny Applications for the R Package Luminescence
+#'
+#' A collection of shiny applications for the R package Luminescence. 
+#' These mainly, but not exclusively, include applications for plotting chronometric 
+#' data from e.g. luminescence or radiocarbon dating. It further provides access to 
+#' bootstraps tooltip and popover functionality as well as a binding to JSColor.
+#'
+#' In addition to its main purpose of providing convenient access to the Luminescence
+#' shiny applications (see \code{\link{app_RLum}}) this package also provides further functions to extend the 
+#' functionality of shiny. From the Bootstrap framework the JavaScript tooltip and popover
+#' components can be added to any shiny application via \code{\link{tooltip}} and \code{\link{popover}}.
+#' It further provides a custom input binding to the JavaScript/HTML color picker JSColor.
+#' Offering access to most options provided by the JSColor API the function \code{\link{jscolorInput}}
+#' is easily implemented in a shiny app. RGB colors are returned as hex values and can be 
+#' directly used in R's base plotting functions without the need of any format conversion.
+#'
+#' @name RLumShiny-package
+#' @aliases RLumShiny
+#' @docType package
+#' @import Luminescence shiny digest googleVis RCurl
+NULL
diff --git a/R/app_RLum.R b/R/app_RLum.R
@@ -2,17 +2,25 @@
 #' 
 #' A wrapper for \code{\link{runApp}} to start interactive shiny apps for the R package Luminescence.
 #' 
+#' The RLumShiny package provides a single function from which all shiny apps can be started: \code{app_RLum()}. 
+#' It essentially only takes one argument, which is a unique keyword specifying which application to start. 
+#' See the table below for a list of available shiny apps and which keywords to use.
+#' 
 #' \tabular{lcl}{
-#' \bold{Application name:} \tab    \tab \bold{Function:} \cr
-#' abanico \tab -> \tab \code{\link{plot_AbanicoPlot}} \cr
-#' histogram \tab -> \tab \code{\link{plot_Histogram}} \cr
-#' KDE \tab -> \tab \code{\link{plot_KDE}} \cr
-#' radialplot \tab -> \tab \code{\link{plot_RadialPlot}} \cr
-#' doserecovery \tab -> \tab \code{\link{plot_DRTResults}} \cr
-#' cosmicdose \tab ->  \tab \code{\link{calc_CosmicDoseRate}}
+#' \bold{Application name:} \tab  \bold{Keyword:}  \tab \bold{Function:} \cr
+#' Abanico Plot \tab \emph{abanico} \tab \code{\link{plot_AbanicoPlot}} \cr
+#' Histogram \tab \emph{histogram} \tab \code{\link{plot_Histogram}} \cr
+#' Kernel Density Estimate Plot \tab \emph{KDE} \tab \code{\link{plot_KDE}} \cr
+#' Radial Plot \tab \emph{radialplot} \tab \code{\link{plot_RadialPlot}} \cr
+#' Dose Recovery Test \tab \emph{doserecovery} \tab \code{\link{plot_DRTResults}} \cr
+#' Cosmic Dose Rate \tab \emph{cosmicdose}  \tab \code{\link{calc_CosmicDoseRate}}
 #' }
 #' 
-#' @param app \code{\link{character}} (required): name of the RLum app to start. See details for a list
+#' The \code{app_RLum()} function is just a wrapper for \code{\link{runApp}}. 
+#' Via the \code{...} argument further arguments can be directly passed to \code{\link{runApp}}. 
+#' See \code{?shiny::runApp} for further details on valid arguments.
+#' 
+#' @param app \code{\link{character}} (required): name of the application to start. See details for a list
 #' of available apps.
 #' @param ... further arguments to pass to \code{\link{runApp}}
 #' @author Christoph Burow, University of Cologne (Germany)

diff --git a/cran-comments.md b/cran-comments.md
@@ -0,0 +1,25 @@
+## Resubmission
+This is a resubmission. In this version I have:
+
+* Referred in the DESCRIPTION to other packages and external libraries in single quotes.
+
+* Made clear in the DESCRIPTION that this package includes the 'jscolor.js' library.
+
+* Removed the LICENSE file and the reference in the DESCRIPTION
+
+* Added a LICENSE.note file to include comments on the licensing
+
+## Test environments
+* local Windows 8 x64 install, R-devel (2015-03-27 r68108)
+* ubuntu 14.04 (VM), R 3.1.3
+
+## R CMD check results
+There were no ERRORs or WARNINGs.
+
+There was 1 NOTE:
+
+* checking CRAN incoming feasibility ... NOTE
+  Maintainer: 'Christoph Burow <christoph.burow@uni-koeln.de>'
+  New submission
+
+  This is a new submission.
diff --git a/inst/shiny/KDE/ui.R b/inst/shiny/KDE/ui.R
@@ -324,7 +324,7 @@ pageWithSidebar(
                                         br(),
                                         a(href = "https://forum.r-luminescence.de", "Message board", target="_blank"),
                                         br(),
-                                        a(href = "https://zerk.canopus.uberspace.de/R.Lum", "Online application", target="_blank"),
+                                        a(href = "http://zerk.canopus.uberspace.de/R.Lum", "Online application", target="_blank"),
                                         br(),hr(),
                                         img(src='GitHub-Mark-32px.png', width='32px', height='32px'),
                                         br(),

diff --git a/inst/shiny/abanico/ui.R b/inst/shiny/abanico/ui.R
@@ -793,7 +793,7 @@ pageWithSidebar(
                                         br(),
                                         a(href = "https://forum.r-luminescence.de", "Message board", target="_blank"),
                                         br(),
-                                        a(href = "https://zerk.canopus.uberspace.de/R.Lum", "Online application", target="_blank"),
+                                        a(href = "http://zerk.canopus.uberspace.de/R.Lum", "Online application", target="_blank"),
                                         br(),hr(),
                                         img(src='GitHub-Mark-32px.png', width='32px', height='32px'),
                                         br(),

diff --git a/inst/shiny/doserecovery/ui.R b/inst/shiny/doserecovery/ui.R
@@ -359,7 +359,7 @@ pageWithSidebar(
                                         br(),
                                         a(href = "https://forum.r-luminescence.de", "Message board", target="_blank"),
                                         br(),
-                                        a(href = "https://zerk.canopus.uberspace.de/R.Lum", "Online application", target="_blank"),
+                                        a(href = "http://zerk.canopus.uberspace.de/R.Lum", "Online application", target="_blank"),
                                         br(),hr(),
                                         img(src='GitHub-Mark-32px.png', width='32px', height='32px'),
                                         br(),

diff --git a/inst/shiny/histogram/ui.R b/inst/shiny/histogram/ui.R
@@ -323,7 +323,7 @@ pageWithSidebar(
                                         br(),
                                         a(href = "https://forum.r-luminescence.de", "Message board", target="_blank"),
                                         br(),
-                                        a(href = "https://zerk.canopus.uberspace.de/R.Lum", "Online application", target="_blank"),
+                                        a(href = "http://zerk.canopus.uberspace.de/R.Lum", "Online application", target="_blank"),
                                         br(),hr(),
                                         img(src='GitHub-Mark-32px.png', width='32px', height='32px'),
                                         br(),

diff --git a/inst/shiny/radialplot/ui.R b/inst/shiny/radialplot/ui.R
@@ -585,7 +585,7 @@ pageWithSidebar(
                                         br(),
                                         a(href = "https://forum.r-luminescence.de", "Message board", target="_blank"),
                                         br(),
-                                        a(href = "https://zerk.canopus.uberspace.de/R.Lum", "Online application", target="_blank"),
+                                        a(href = "http://zerk.canopus.uberspace.de/R.Lum", "Online application", target="_blank"),
                                         br(),hr(),
                                         img(src='GitHub-Mark-32px.png', width='32px', height='32px'),
                                         br(),

diff --git a/inst/www/jscolor/LICENSE b/inst/www/jscolor/LICENSE
diff --git a/inst/www/jscolor_inputBinding.js b/inst/www/jscolor_inputBinding.js
@@ -1,4 +1,4 @@
-//input binding
+// JSColor shiny input binding
 var jscolor = new Shiny.InputBinding();
 $.extend(jscolor, {
   find: function(scope) {