diff --git a/CONVENTIONS b/CONVENTIONS deleted file mode 100644 index 462d503..0000000 --- a/CONVENTIONS +++ /dev/null @@ -1,7 +0,0 @@ -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. \ No newline at end of file diff --git a/DESCRIPTION b/DESCRIPTION index e563b75..b4b2642 100644 --- a/DESCRIPTION +++ b/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 VignetteBuilder: knitr @@ -11,7 +11,6 @@ Imports: Suggests: testthat, knitr, - devtools, ape, networkD3, yaml, @@ -19,7 +18,10 @@ Suggests: 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, diff --git a/R/node_methods.R b/R/node_methods.R index 1b52609..c184780 100644 --- a/R/node_methods.R +++ b/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 } diff --git a/README.md b/README.md index fc69c95..07d918e 100644 --- a/README.md +++ b/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. \ No newline at end of file diff --git a/data.tree.Rproj b/data.tree.Rproj index 6ccebc5..a52ec59 100644 --- a/data.tree.Rproj +++ b/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 diff --git a/vignettes/applications.Rmd b/vignettes/applications.Rmd index e3d9d0a..2ec4de6 100644 --- a/vignettes/applications.Rmd +++ b/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() ``` diff --git a/vignettes/assets/bubbles.html b/vignettes/assets/bubbles.html deleted file mode 100644 index c648fcf..0000000 --- a/vignettes/assets/bubbles.html +++ /dev/null @@ -1,17 +0,0 @@ - - - - - - - - - - -
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