Blog Archives

Mongolite 2.0: GridFS, connection pooling, and more

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...

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phylotaR: Retrieve Orthologous Sequences from GenBank

phylotaR: Retrieve Orthologous Sequences from GenBank

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...

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Extracting and Processing eBird Data

Extracting and Processing eBird Data

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...

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A package for dimensionality reduction of large data

A package for dimensionality reduction of large data

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...

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

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

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...

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rOpenSci Educators Collaborative: What Educational Resources Work Well and Why?

rOpenSci Educators Collaborative: What Educational Resources Work Well and Why?

In the first post of this series, we sketched out some of the common challenges faced by educators who teach with R across scientific domains. In this post, we delve into what makes a “good” educational resource for teaching science with R. For instructors teaching sciences with R, there are a number of open educational resources that they can reuse,...

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rOpenSci Educators Collaborative: What Are The Challenges When Teaching Science With R?

rOpenSci Educators Collaborative: What Are The Challenges When Teaching Science With R?

Educators who teach science using R tend to face common pedagogical problems, regardless of their scientific domain. Yet instructors who teach with R often feel isolated at their institutions. They may be the only ones in their de...

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Gifski on CRAN: the fastest GIF encoder in the universe

Gifski on CRAN: the fastest GIF encoder in the universe

The gifski package which was demonstrated in May at eRum 2018 in Budapest is now on CRAN. Gifski is a simple but powerful package which can hopefully take away an important performance bottleneck for generating animated graphics in R. What is Gifski Gifski is a multi-threaded high-quality GIF encoder written in Rust. It can create animated GIF images with thousands of...

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What’s inside? pkginspector provides helpful tools for inspecting package contents

What’s inside? pkginspector provides helpful tools for inspecting package contents

R packages are widely used in science, yet the code behind them often does not come under scrutiny. To address this lack, rOpenSci has been a pioneer in developing a peer review process for R packages. The goal of pkginspector is to help that process by providing a means to better understand the internal structure of R packages. It...

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phylogram: dendrograms for evolutionary analysis

phylogram: dendrograms for evolutionary analysis

Evolutionary biologists are increasingly using R for building, editing and visualizing phylogenetic trees. The reproducible code-based workflow and comprehensive array of tools available in packages such as ape, phangorn and phytools make R an ideal platform for phylogenetic analysis. Yet the many different tree formats are not well integrated, as pointed out in a recent post. The standard data structure for phylogenies in R is the “phylo” object, a memory...

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