Sharing data sets for collaboration or publication has always been challenging, but it’s become increasingly problematic as complex and high dimensional data sets have become ubiquitous in the life sciences. Studies are large and time consuming; data collection takes time, data analysis is a moving target, as is the software used to carry it out.

In the second post of the series where we obtained data fromeBird wedetermined what birds were observed in the county of Constance, and wecomplemented this knowledge with some taxonomic and trait information inthe fourth post of theseries.

A while ago weonboarded anexciting package, codemetarby Carl Boettiger. codemetar is an R specificinformation collector and parser for the CodeMetaproject. In particular, codemetar candigest metadata about an R package in order to fill the termsrecognized by CodeMeta. This meansextracting information from DESCRIPTION but also from e.g. continuousintegration ¹ badges in the README!

You might have read my blog post analyzing the social weather ofrOpenScionboarding,based on a text analysis of GitHub issues. I extracted text out ofMarkdown-formatted threads with regular expressions. I basicallyhammered away at the issues using tools I was familiar with until itworked! Now I know there’s a much better and cleaner way, that I’llpresent in this note. Read on if you want to extract insights abouttext, code, links, etc.

Thanks to the second post of the series where we obtained data fromeBird we knowwhat birds were observed in the county of Constance. Now, not allspecies’ names mean a lot to me, and even if they did, there are a lotof them.

In this new post, we’re taking a break from modern birding data in ourbirder’s series… let’s exploregorgeous drawings from a natural history collection!

rgbif was seven years old yesterday! 🔗What is rgbif? rgbif gives you access to data from the Global Biodiversity Information Facility (GBIF) via their API.

Thanks to the first post of theseries we knowwhere to observe birds near Radolfzell’s Max Planck Institute forOrnithology, so we could go and do that! Or we can stay behind ourlaptops and take advantage of eBird, afantastic bird sightings aggregator!

This week version 2.0 of the mongolite package has been released to CRAN. Major new features in this release include support for MongoDB 4.0, GridFS, running database commands, and connection pooling. Mongolite is primarily an easy-to-use client to get data in and out of MongoDB. However it supports increasingly many advanced features like aggregation, indexing, map-reduce, streaming, encryption, and enterprise authentication.

This post is the 1st post of a series showcasing various rOpenScipackages as if Maëlle were a birder trying to make the most of R ingeneral and rOpenSci in particular. Although the series use cases willmostly feature birds , it’ll be the occasion to highlight rOpenSci’spackages that are more widely applicable, so read on no matter what yourfield is! Moreoever, each post should stand on its own.

In this technote I will outline what phylotaR was developed for, how to install it and how to run it with some simple examples. 🔗What is phylotaR? In any phylogenetic analysis it is important to identify sequences that share the same orthology – homologous sequences separated by speciation events. This is often performed by simply searching an online sequence repository using sequence labels.