Publications by rOpenSci - open tools for open science
Extracting eBird Data from a Polygon
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 chunks of the dataset based on various spatial, temporal, or taxonomic fil...
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2 Months in 2 Minutes – rOpenSci News, April 2020
rOpenSci HQ The recording, collaborative notes and links to community discussion and resources are up for our latest Community Call on Maintaining an R package. Panel moderated by Julia Silge included Elin Waring, Erin Grand, Leonardo Collado-Torres, and Scott Chamberlain. Software Peer Review 1 staff-contributed package passed software peer re...
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Automatic Code Cleaning in R with Rclean
Leave the code cleaner than you found it. – R.C. Martin in Clean Code The R language has become very popular among scientists and analysts because it enables the rapid development of software and empowers scientific investigation. However, regardless of the language used, data analysis is usually complicated. Because of various project complex...
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Miscellaneous Wisdom about R Markdown & Hugo Gained from Work on our Website
Whilst working on the blog guide, Stefanie Butland and I consolidated knowledge we had already gained, but it was also the opportunity to up our Rmd/Hugo technical game. Our website uses Hugo but not blogdown1 to render posts: every post is based on an .md file that is either written directly or knit from an .Rmd file. We wanted to provide clear ...
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Highlights of Hugo Code Highlighting
Thanks to a quite overdue update of Hugo on our build system1, our website can now harness the full power of Hugo code highlighting for Markdown-based content. What’s code highlighting apart from the reason behind a tongue-twister in this post title? In this post we shall explain how Hugo’s code highlighter, Chroma, helps you prettify your co...
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A Roundup of R Tools for Handling BibTeX
Our website is based on Markdown content rendered with Hugo. Markdown content is in some cases knit from R Markdown, but with less functionality than if one rendered R Markdown to html as in the blogdown default. In particular, we cannot use the usual BibTex + CSL + Pandoc-citeproc dance to handle a bibliography. Thankfully, using the rOpenSci pa...
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When Field or Lab Work is not an Option – Leveraging Open Data Resources for Remote Research
The COVID-19 pandemic has dramatically impacted all of our lives in a very short period of time. Spring and summer are usually very busy as students prepare to go the field to engage in various data collection efforts. The pandemic has also disrupted these carefully planned activities as travel is suspended and local and remote field stations hav...
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Superior svg graphics rendering in R, and why it matters
This week we released a major new version of the rsvg package on CRAN. This package provides R bindings to librsvg2 which is a powerful system library for rendering svg images into bitmaps that can be displayed, or use for further processing in for example the magick package. The biggest change in this release is the R package on Windows and MacO...
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2 Months in 2 Minutes – rOpenSci News, June 2020
rOpenSci HQ The rOpenSci team, together with ten expert community members, put together a post: When Field or Lab Work is not an Option – Leveraging Open Data Resources for Remote Research. We highlighted examples of how specific collections of packages are being used right now in fields as varied as archaeology and climate science and compiled...
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A better way to manage your Github personal access tokens
We have been working hard behind the scenes on the upcoming release of our new git package named gert, a joint effort from rOpenSci and the Tidyverse team. One of the main features of gert is the out-of-the-box authentication mechanism, which is provided via the new credentials package. Among other things, the credentials package makes it possibl...
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