Posts with the "r" tag

Generating reasonable starting trees for complex phylogenetic analyses

December 11, 2018

By:   April Wright

I never really thought I would write an R package. I use R pretty casually. Then, this year, I was invited to participate during the last week of the Analytical Paleobiology short course, an intensive month-long experience in quantitative paleontology. I was thrilled to be invited. But I got a slight sinking feeling in my stomach when I realized all the materials were in R. And so I, a Pythonista, decided I would spend some of my maternity leave writing R packages to try to blend in with students who had spent the month living and breathing R.

Community Call - Governance strategies for open source research software projects

December 5, 2018

By:   Dan Sholler  |   Stefanie Butland

🎤 Dan Sholler, rOpenSci Postdoctoral Fellow 🕘 Tuesday, December 18, 2018, 10-11AM PST; 7-8PM CET (find your timezone) ☎️ Details for joining the Community Call. Everyone is welcome. No RSVP needed. Researchers use open source software for the capabilities it provides, such as streamlined data access and analysis and interoperability with other pieces of the scientific computing ecosystem. For most complex software, generating these technical capabilities requires building and governing a community via sound management practices, activities that are often less visible than code contributions and other software development work.

Detecting spatiotemporal groups in relocation data with spatsoc

December 4, 2018

By:   Alec Robitaille  |   Quinn Webber  |   Eric Vander Wal

spatsoc is an R package written by Alec Robitaille, Quinn Webber and Eric Vander Wal of the Wildlife Evolutionary Ecology Lab (WEEL) at Memorial University of Newfoundland. It is the lab’s first R package and was recently accepted through the rOpenSci onboarding process with a big thanks to reviewers Priscilla Minotti and Filipe Teixeira, and editor Lincoln Mullen. spatsoc started as a single function (what would eventually become group_pts) written by Alec in 2017 to help answer some of the questions that Quinn and Eric were asking about how animal social structure is related to spatial processes.

rnoaa: new data sources and NCDC units

December 4, 2018

By:   Scott Chamberlain

We’ve just released a new version of rnoaa with A LOT of changes. Check out the release notes for a complete list of changes. We’ll highlight a few things in this post: New data sources in the package NCDC units added to the output of ncdc() Links: rnoaa source code: https://github.com/ropensci/rnoaa rnoaa on CRAN: https://cran.rstudio.com/web/packages/rnoaa/ Installation Install the lastest from CRAN install.packages("rnoaa") Some binaries are not up yet on CRAN - you can also install from GitHub:

restez: Query GenBank locally

December 3, 2018

By:   Dom Bennett

What is restez? R packages for interacting with the National Center for Biotechnology Information (NCBI) have, to-date, depended on API query calls via NCBI’s Entrez. For computational analyses that require the automated look-up of reams of biological sequence data, piecemeal querying via bandwith-limited requests is evidently not ideal. These queries are not only slow, but they depend on network connections and the remote server’s consistent behaviour. Additionally, users who make very large requests over extended periods of time run the risk of being blocked.

Page 1 of 41