Posts with the "software" 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.

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.

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.

The Antarctic/Southern Ocean rOpenSci community

November 13, 2018

By:   Ben Raymond  |   Michael Sumner  |   on behalf of the community

Antarctic/Southern Ocean science and rOpenSci Collaboration and reproducibility are fundamental to Antarctic and Southern Ocean science, and the value of data to Antarctic science has long been promoted. The Antarctic Treaty (which came into force in 1961) included the provision that scientific observations and results from Antarctica should be openly shared. The high cost and difficulty of acquisition means that data tend to be re-used for different studies once collected.

outcomerate: Transparent Communication of Quality in Social Surveys

October 2, 2018

By:   Rafael Pilliard Hellwig

Background Surveys are ubiquitous in the social sciences, and the best of them are meticulously planned out. Statisticians often decide on a sample size based on a theoretical design, and then proceed to inflate this number to account for “sample losses”. This ensures that the desired sample size is achieved, even in the presence of non-response. Factors that reduce the pool of interviews include participant refusals, inability to contact respondents, deaths, and frame inaccuracies.

Page 1 of 12