Working together to push science forward
Happy rOpenSci users can be found at
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. A samping of use cases covered in rgbif: Search for datasets Get metrics on usage of datasets Get metadata about organizations providing data to GBIF Search taxonomic names Get quick taxonomic name suggestions Search occurrences by taxonomic name/country/collector/etc. Download occurrences by taxonomic name/country/collector/etc....
Thanks to the first post of the series we know where to observe birds near Radolfzell’s Max Planck Institute for Ornithology, so we could go and do that! Or we can stay behind our laptops and take advantage of eBird, a fantastic bird sightings aggregator! As explained by Matt Strimas-Mackey in his recent blog post, “The eBird database currently contains over 500 million records of bird sightings, spanning every country and over 98% of species, making it an extremely valuable resource for bird research and conservation....
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. The mongolite user manual provides a great introduction with details and worked examples....
This post is the 1st post of a series showcasing various rOpenSci packages as if Maëlle were a birder trying to make the most of R in general and rOpenSci in particular. Although the series use cases will mostly feature birds, it’ll be the occasion to highlight rOpenSci’s packages that are more widely applicable, so read on no matter what your field 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. Relying solely on sequence labels, however, can miss sequences that have either not been labelled, have unanticipated names or have been mislabelled....
Happy rOpenSci users can be found at