Merge branch 'dev'

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: data.tree
 Type: Package
 Title: General Purpose Hierarchical Data Structure
-Version: 0.1.9
-Date: 2015-08-01
+Version: 0.2.0-2
+Date: 2015-09-07
 Author: Christoph Glur
 Maintainer: Christoph Glur <christoph.glur@ipub.com>
 VignetteBuilder: knitr
@@ -11,15 +11,17 @@ Imports:
 Suggests:
     testthat, 
     knitr, 
-    devtools,
     ape, 
     networkD3, 
     yaml, 
     jsonlite, 
     DiagrammeR, 
     igraph,
     treemap,
-    curl
+    curl,
+    doParallel,
+    foreach,
+    htmlwidgets
 Enhances:
 Description: Create tree structures from hierarchical data, and use the utility 
     methods to traverse the tree in various orders. Aggregate, cumulate, print, convert to and from data.frame, 

R/node_methods.R

@@ -39,7 +39,7 @@ print.Node <- function(x, ..., pruneMethod = c("simple", "dist", NULL), limit =
     }
   } else if(!x$isRoot) {
       #clone s.t. x is root (for pretty level names)
-      x <- Clone(x, pruneFun = pruneFun, attributes = TRUE)
+      x <- Clone(x, attributes = TRUE)
       x$parent <- NULL
   }
 

README.md

@@ -17,3 +17,14 @@ The package provides functionality to convert from and to various formats such a
 
 # NOTE:
 The latest from github has some breaking changes compared to CRAN. See [NEWS](https://github.com/gluc/data.tree/blob/master/NEWS) for details.
+
+
+# Conventions:
+
+Coding Conventions: Google Style Guide, see https://google-styleguide.googlecode.com/svn/trunk/Rguide.xml
+
+Versioning Conventions: SemanticVersioning. See http://semver.org/ for details
+
+Branching Conventions: GitFlow. See https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow
+
+Pull Requests: Very welcome. Please branch from the dev branch if possible.

data.tree.Rproj

@@ -13,7 +13,6 @@ RnwWeave: knitr
 LaTeX: pdfLaTeX
 
 BuildType: Package
-PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
 PackageBuildArgs: --resave-data
 PackageBuildBinaryArgs: --resave-data

vignettes/applications.Rmd

@@ -768,7 +768,7 @@ Here, it was particularly simple, because the underlying JSON structure is regul
 What follows has nothing to do with data.tree anymore. We simply provide the bubble chart printing for your enjoyment. In order to run it yourself, you need to install the bubbles package from github:
 
 
-```{r}
+```{r, eval = FALSE}
 
 devtools::install_github("jcheng5/bubbles@6724e43f5e")
 library(scales)
@@ -787,6 +787,8 @@ bubbles(
 )
 ```
 
+![bubbles](assets/bubbles.jpg)
+
 
 # File Explorer (System Utilities, visualisation)
 
@@ -829,8 +831,7 @@ print(fileStructure, "mode", "size", limit = 25)
 
 Finally, we can display the files by timelyportfolio's listviewer. As it's not on CRAN, we only display a screenshot of the widget in in this vignette. This is not half as fun as the interactive widget, of course. So please try it out for yourself to see it in action.
 
-```{r}
-
+```{r, eval = FALSE}
 
 #This requires listviewer, which is available only on github
 devtools::install_github("timelyportfolio/listviewer")
@@ -842,7 +843,9 @@ jsonedit(l)
 
 ```
 
+![listviewer](assets/listviewer.jpg)
 
+(Run the code yourself to see the widget in action)
 
 # Gene Defect (genetics, probabilities, multi-generation models)
 
@@ -993,12 +996,10 @@ It is straight forward to parallelise the simulation. If, as in this example, yo
 ```{r}
 library(foreach)
 library(doParallel)
-registerDoParallel(makeCluster(3))
+registerDoParallel(makeCluster(2))
 #On Linux, there are other alternatives, e.g.: library(doMC);  registerDoMC(3)
 
 system.time(x <- foreach (i = 1:100, .packages = "data.tree") %dopar% FreqLastGen(GenerateChildrenTree()))
-x <- as.numeric(x)
-
 stopImplicitCluster()
 ```