Author: rOpenSci - open tools for open science

Feed: R-bloggers. Author: rOpenSci - open tools for open science. 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 MacOS now includes the latest librsvg 2.48.4. This is a major upgrade; the librsvg2 rendering engine has been completely rewritten in Rust using components from Mozilla Servo. This ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. 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 package RefManageR, we can still make our own bibliography from a BibTeX file without formatting references by hand.In this post we shall present our custom workflow for inserting citations, as well as more mainstream tools ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. Leave the code cleaner than you found it. – R.C. Martin in Clean Code The R language has become very popular among scientists and analystsbecause it enables the rapid development of software and empowersscientific investigation. However, regardless of the language used,data analysis is usually complicated. Because of various projectcomplexities and time constraints, analytical software often reflectsthese challenges. “What did I measure? What analyses are relevant tothe study? Do I need to transform the data? What’s the function for theanalysis I want to run?” Although many researchers see the value inlearning ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. 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 review. On March 16, we paused new submissions for software peer review for 30 days (possibly longer) in the interest of reducing load on reviewers and editors in light of the COVID-19 crisis. Software 5 new packages from the community and ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. 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 filters. I’m often asked “how do I extract data from within a polygon?” (usually “polygon” is replaced by “shapefile”, but I try to avoid that word since there’s good ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. 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 that, as indicated in the README of the software review repo, in the interest of reducing load on reviewers and editors as we manage the COVID-19 crisis, rOpenSci is temporarily pausing new submissions for software peer review for 30 days (and possibly longer). Please ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. 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 foray into the glorious process of publishing a book with bookdown, and Maëlle’s second. And oh, we learned a lot. Stef (first-timer) 1. How to collaborate across timezones There is a 9-hour time difference between Maëlle and me for most ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. parzer is a new package forhandling messy geographic coordinates. The first version is now on CRAN,with binaries coming soon hopefully (see note about installation below).The package recently completed rOpenScireview. parzer motivation The idea for this package started with a tweet from NoamRoss(https://twitter.com/noamross/status/1070733367522590721) about 15months ago. The idea being that sometimes you have geographic coordinates in a messyformat, or in many different formats, etc. You can think of it as beingthe package for geographic coordinates thatlubridate is fordates. I started off thinking about wrapping a Javascript library withJeroen’sV8 R package, but ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. “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 professional providers exist (Travis CI, AppVeyor CI, Circle CI, etc.) which offer CI services to the public.Most services offer limited free build contingents for open-source projects.However, it has not been easy for the R community to jump on the train right away ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. 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 routes. This is where we hit a problem for services such as Google or the Open Route Service, that usually only allow a limited number of free routes per day (typically around 1000). So routing is either very time consuming ... Read More