Publications by rOpenSci - open tools for open science
Covidpreprints.com: Automating Website Updates with the europepmc and rAltmetric Packages
At the eLife Sprint in September 2020, we revamped the covidpreprints.com website, which aims at featuring landmark preprints on a timeline of the pandemic. The birth of the project The ongoing COVID-19 pandemic has led to about 35 million confirmed cases and over a million deaths worldwide. The looming spectre of a second wave of the pandemic h...
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2 Months in 2 Minutes – rOpenSci News, October 2020
rOpenSci HQ rOpenSci at R-Ladies Our community manager Stefanie Butland, and one of our software review editors Brooke Anderson, are speaking remotely at an R-Ladies East Lansing meetup Thursday, October 22nd. They will talk about our how to get involved in rOpenSci using our new Contributing Guide as an entry point, and through participating in...
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Searching medRxiv and bioRxiv Preprint Data
Background & motivation medRxiv, as the preprint repository for papers in the medical, clinical, and related health sciences,1 has become a central source of new studies related to the COVID-19 pandemic. As a result, more and more researchers have begun to include medRxiv in the list of bibliographic databases they search as part of systematic re...
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rOpenSci Dev Guide 0.5.0: Updates
rOpenSci Software Peer Review’s guidance has been compiled in an online book for more than one year now. We’ve just released its fifth version. To find out what’s new in our dev guide 0.5.0, you can read the changelog, or this blog post for more digested information. We have resumed activity after a break due to the COVID-19 crisis, but ar...
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Announcing New Software Peer Review Editors: Laura DeCicco, Julia Gustavsen, Mauro Lepore
We are pleased to welcome Laura DeCicco, Julia Gustavsen, and Mauro Lepore to our team of Associate Editors for rOpenSci Software Peer Review. They join Brooke Anderson, Anna Krystalli, Karthik Ram, Noam Ross, Maëlle Salmon, and Melina Vidoni. Lincoln Mullen and Scott Chamberlain are now board alumni. Since 2015, rOpenSci has been running a soft...
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Using Open-Access Tools (rentrez, taxize) to Find Coronaviruses, Their Genetic Sequences, and Their Hosts
Emerging viruses might be on everyone’s mind right now, but as an epidemiologist and disease ecologist I’ve always been interested in how and why pathogens move from animal hosts to humans. The current pandemic of the disease we call COVID-19 is caused by Severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2), a virus that has em...
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Installing V8 is now even easier
Google’s amazing V8 JavaScript/WASM engine is probably one of the most sophisticated open-source software libraries available today. It is used to power the computation in Google Chrome, NodeJS, and also CloudFlare Workers, which make it possible to run code for your website inside the CDN edges. The R package V8 exposes this same engine in R, ...
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fulltext: Behind the Scenes
fulltext is a package I maintain for text-mining the scholarly literature (package docs). You can search for articles, fetch article metadata and abstracts, and fetch full text of some articles. Text-mining the scholarly literature is a research tool used across disciplines. Full text of articles (entire article, not just the abstract) is the gol...
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The Wild World of Data Repositories
How to join this free online event with Kara Woo, Daniella Lowenberg, Matt Jones, Carl Boettiger and Karthik Ram. There is no one-size-fits-all protocol for depositing your research data into a public repository in a way that maximizes its reuse and citation. We’ve assembled a panel that will help you understand the issues and opportunities for...
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Moving away from Travis CI
At rOpenSci, we encourage R package developers to take advantage of Continuous Integration services to automatically check the package on different platforms, with different versions of R. The rOpenSci dev guide dedicates chapter 2 to the topic of Continuous Integration Best Practices, and recommends a few common CI vendors, including Travis CI. ...
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