Mongolite 2.0: GridFS, connection pooling, and more

August 14, 2018

By: Jeroen Ooms

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.

phylotaR: Retrieve Orthologous Sequences from GenBank

August 8, 2018

By: Dom Bennett

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.

Extracting and Processing eBird Data

August 7, 2018

By: Matthew Strimas-Mackey

eBird is an online tool for recording bird observations. The eBird database currently contains over 500 million records of bird sightings, spanning every country and nearly every bird species, making it an extremely valuable resource for bird research and conservation. These data can be used to map the distribution and abundance of species, and assess how species’ ranges are changing over time. This dataset is available for download as a text file; however, this file is huge (over 180 GB!

A package for dimensionality reduction of large data

August 1, 2018

By: Sean Hughes  |  Angela Li  |  Ju Kim  |  Malisa Smith  |  Ted Laderas

Motivation Note: Recently, two new UMAP R packages have appeared. These new packages provide more features than umapr does and they are more actively developed. These packages are: umap, which provides the same Python wrapping function as umapr and also an R implementation, removing the need for the Python version to be installed. It is available on CRAN. uwot, which also provides an R implementation, removing the need for the Python version to be installed.

rOpenSci Educators Collaborative: How Can We Develop a Community of Innovative R Educators?

July 26, 2018

By: Laura Ación  |  Mara Averick  |  Leonardo Collado Torres  |  Auriel Fournier  |  Alison Hill  |  Sean Kross  |  Lincoln Mullen

tl;dr: we propose three calls to action: Share your curricular materials in the open. Participate in the rOpenSci Education profile series. Discuss with us how you want to be involved in rOpenSci Educators’ Collaborative. In previous posts in this series, we identified challenges that individual instructors typically face when teaching science with R, and shared characteristics of effective educational resources to help address these challenges. However, the toughest challenges that educators in this area face are human, rather than technological.

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