Publications by rOpenSci - open tools for open science
Tesseract 4 is here! State of the art OCR in R!
Last week Google and friends released the new major version of their OCR system: Tesseract 4. This release builds upon 2+ years of hard work and has completely overhauled the internal OCR engine. From the tesseract wiki: Tesseract 4.0 includes a new neural network-based recognition engine that delivers significantly higher accuracy (on document ...
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The Antarctic/Southern Ocean rOpenSci community
Antarctic/Southern Ocean science and rOpenSci Collaboration and reproducibility are fundamental to Antarctic and Southern Ocean science, and the value of data to Antarctic science has long been promoted. The Antarctic Treaty (which came into force in 1961) included the provision that scientific observations and results from Antarctica should be o...
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Checklist Recipe – How we created a template to standardize species data
Imagine you are a fish ecologist who compiled a list of fish species for your country. ???? Your list could be useful to others, so you publish it as a supplementary file to an article or in a research repository. That is fantastic, but it might be difficult for others to discover your list or combine it with other lists of species. Luckily there...
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Co-localization analysis of fluorescence microscopy images
A few months ago, I wasn’t sure what to expect when looking at fluorescence microscopy images in published papers. I looked at the accompanying graph to understand the data or the point the authors were trying to make. Often, the graph represents one or more measures of the so-called co-localization, but I couldn’t figure out how to interpret...
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Community Call Summary – Code Review in the Lab
Although there are increasing incentives and pressures for researchers to share code (even for projects that are not essentially computational), practices vary widely and standards are mostly non-existent. The practice of reviewing code then falls to researchers and research groups before publication. With that in mind, rOpenSci hosted a discussi...
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restez: Query GenBank locally
What is restez? R packages for interacting with the National Center for Biotechnology Information (NCBI) have, to-date, depended on API query calls via NCBI’s Entrez. For computational analyses that require the automated look-up of reams of biological sequence data, piecemeal querying via bandwith-limited requests is evidently not ideal. These ...
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rnoaa: new data sources and NCDC units
We’ve just released a new version of rnoaa with A LOT of changes. Check out the release notes for a complete list of changes. We’ll highlight a few things in this post: New data sources in the package NCDC units added to the output of ncdc() Links: rnoaa source code: https://github.com/ropensci/rnoaa rnoaa on CRAN: https://cran.rstudio.com...
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Detecting spatiotemporal groups in relocation data with spatsoc
spatsoc is an R package written by Alec Robitaille, Quinn Webber and Eric Vander Wal of the Wildlife Evolutionary Ecology Lab (WEEL) at Memorial University of Newfoundland. It is the lab’s first R package and was recently accepted through the rOpenSci onboarding process with a big thanks to reviewers Priscilla Minotti and Filipe Teixeira, and e...
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Community Call – Governance strategies for open source research software projects
???? Dan Sholler, rOpenSci Postdoctoral Fellow ???? Tuesday, December 18, 2018, 10-11AM PST; 7-8PM CET (find your timezone) ☎️ Details for joining the Community Call. Everyone is welcome. No RSVP needed. Researchers use open source software for the capabilities it provides, such as streamlined data access and analysis and interoperability wit...
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Generating reasonable starting trees for complex phylogenetic analyses
I never really thought I would write an R package. I use R pretty casually. Then, this year, I was invited to participate during the last week of the Analytical Paleobiology short course, an intensive month-long experience in quantitative paleontology. I was thrilled to be invited. But I got a slight sinking feeling in my stomach when I realized ...
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