treeio: Phylogenetic data integration

  Guangchuang Yu   | MAY 17, 2018

Phylogenetic trees are commonly used to present evolutionary relationships of species. Newick is the de facto format in phylogenetic for representing tree(s). Nexus format incorporates Newick tree text with related information organized into separated units known as blocks. For the R community, we have ape and phylobase packages to import trees from Newick and Nexus formats. However, analysis results (tree + analysis findings) from widely used software packages in this field are not well supported.

The social weather of rOpenSci onboarding system

  Maëlle Salmon   | MAY 10, 2018

Our onboarding process ensures that packages contributed by the community undergo a transparent, constructive, non adversarial and open review process. Before even submitting my first R package to rOpenSci onboarding system in December 2015, I spent a fair amount of time reading through previous issue threads in order to assess whether onboarding was a friendly place for me: a newbie, very motivated to learn more but a newbie nonetheless. I soon got the feeling that yes, onboarding would help me make my package better without ever making me feel inadequate.

How much work is onboarding?

  Maëlle Salmon   |   Noam Ross   | MAY 3, 2018

Our onboarding process, that ensures that packages contributed by the community undergo a transparent, constructive, non adversarial and open review process, involves a lot of work from many actors: authors, reviewers and editors; but how much work? Managing the effort involved in the peer-review process is a major part of ensuring its sustainability and quality. In this post, we’ll take a look at the effort put in by participants in the review process, and also learn something about exploring GitHub data along the way.

Our package reviews in review: Introducing a 3-post series about software onboarding data

  Maëlle Salmon   | APRIL 26, 2018

On March the 17th I had the honor to give a keynote talk about rOpenSci’s package onboarding system at the satRday conference in Cape Town, entitled “Our package reviews in review: introducing and analyzing rOpenSci onboarding system”. You can watch its recording, skim through the corresponding slides or… read this series! What is rOpenSci onboarding? rOpenSci’s suite of packages is partly contributed by staff members and partly contributed by community members, which means the suite stems from a great diversity of skills and experience of developers.

Rectangling onboarding

  Maëlle Salmon   | APRIL 26, 2018

Our onboarding reviews, that ensure that packages contributed by the community undergo a transparent, constructive, non adversarial and open review process, take place in the issue tracker of a GitHub repository. Development of the packages we onboard also takes place in the open, most often in GitHub repositories. Therefore, when wanting to get data about our onboarding system for giving a data-driven overview, my mission was to extract data from GitHub and git repositories, and to put it into nice rectangles (as defined by Jenny Bryan) ready for analysis.

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