One of the first things I took on when I started at the Cornell Lab of Ornithology was creating the auk R package for accessing eBird data. The entire eBird dataset can be downloaded as a massive text file, called the eBird Basic Dataset (EBD), and auk pulls out manageable ... [Read more...]

rOpenSci Software Peer Review’s guidance has been compiled in an online book for more than one year now. We’ve just released its fourth version. To find out what’s new in our dev guide 0.4.0, you can read the changelog, or this blog post for more digested information. Note ... [Read more...]

After soliciting, reviewing, and publishing over 100 blog posts and tech notes by rOpenSci community members, we have created the rOpenSci Blog Guide for Authors and Editors to address many frequently asked questions and frequently given suggestions. Technically, we structured the content as a bookdown gitbook. It was Stef’s first ... [Read more...]

parzer is a new package for handling messy geographic coordinates. The first version is now on CRAN, with binaries coming soon hopefully (see note about installation below). The package recently completed rOpenSci review. parzer motivation The idea for this package started with a tweet from Noam Ross (https://twitter.com/... [Read more...]

“Continuous Integration” (CI) has become a standard for proper software development. Checking the integrity of software after changes have been made is essential to ensure its proper functionality. Also, CI helps catch problems introduced by dependencies early when executed on a regular basis (usually done via scheduled CRON runs). Multiple ... [Read more...]

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With services like Google Maps, finding the fastest route from A to B has become quick, cheap, and easy. Not just for driving but walking, cycling and public transport too. But in the field of transport studies, we often want not only a single route, but thousands or millions of ... [Read more...]

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rOpenSci HQ On behalf of rOpenSci, thank you to everyone who has contributed their creativity, curiosity, smarts, and time in the last year. Read our Thank You, 2019. Software Peer Review 3 community-contributed packages passed... [Read more...]

Dealing with taxonomic inconsistencies within and across datasets is a fundamental challenge of ecology and evolutionary biology. Accounting for species synonyms, taxa splitting and unification is especially important as aggregation of data across time and different data sources becomes increasingly common. One potentially powerful approach for addressing these issues is ... [Read more...]

It was the best of times, it was the worst of times. Dickens might have meant it figuratively, but in the case of the rOpenSci OzUnconf 2019, we mean it literally. Set to the backdrop of a national emergency that is still ongoing from 11-13 December, our participants came from across ... [Read more...]

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babette 1 is a package to work with BEAST2 2, a software platform for Bayesian evolutionary analysis from R. babette is a spin-off of my own academic research. As a PhD I work on models of diversification: mathematical descriptions of how species form new species. Instead of working on a species’ individuals, ... [Read more...]

One year ago, we released our new Code of Conduct. At that time, the Code of Conduct Committee (authors of this post) agreed to do an annual review of the text, reporting form, and our internal guidelines. We have made one change to the Code of Conduct text. Because some ... [Read more...]

In January 2019, we announced the release of rOpenSci’s Code of Conduct version 2.0. This includes a named Committee, greater detail about unacceptable behaviors, instructions on how to make a report, and information on how reports are handled. We are committed to transparency with our community while upholding of victims and ... [Read more...]

We mean it. On behalf of rOpenSci, thank you to everyone who has contributed their creativity, curiosity, smarts, and time in the last year. We are fortunate to have paid staff who work to build technical and social infrastructure to... [Read more...]

Want to get some hands-on insights into running an open source community? Here’s an opportunity to work with me, rOpenSci’s Community Manager, on some non-code community-related work. I am looking for someone to work 1 day a week ... [Read more...]

rOpenSci HQ rOpenSci Announces a New $896k Award From The Gordon and Betty Moore Foundation to Improve the Scientific Package Ecosystem for R. We’re excited to announce a new member of our team! Introducing Mark Padgham, rOpenSci’s new Software Research Scientist NumFOCUS recognizes Melina Vidoni and Will Landau ... [Read more...]

Last year we reported on the joy of using commonmark and xml2 to parse Markdown content, like the source of this website built with Hugo, in particular to extract links, at the time merely to count them. How about we go a bit further and use the same approach to ... [Read more...]

Testing is a crucial component to any software package. Testing makes sure that your code does what you expect it to do; and importantly, makes it safer to make changes moving forward because a good test suite will tell you if a change has broken existing functionality. Our recent community ... [Read more...]