Author: rOpenSci - open tools for open science

Feed: R-bloggers. Author: rOpenSci - open tools for open science. 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 to resolve scientific names to taxonomic identifiers that follow a consistent taxonomic concept. In such a workflow, data from one of the many taxonomic providers (e.g. Integrated Taxonomic Information System , Catalogue of Life , National Center for Biological Information ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. 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 Australia as well as New Zealand, Japan, India and Indonesia. An rOpenSci unconference (unconf) is about building – building software, tools, but more importantly community. It operates on the premise that we all belong. Joining the R community doesn’t ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. The latest version of the rOpenSci av package includes some useful new tools for working with audio data. We have added functions for reading, cutting, converting, transforming, and plotting audio data in any popular audio / video format (mp3, mkv, aac, etc). The functionality can either be used by itself, or to prepare audio data for further analysis in R using other packages. We hope this clears an important hurdle to use R for research on speech, music, and whale mating calls. Audio analysis in R CRAN has serveral cool ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. 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 people who have experienced abuse prefer not to label themselves as a victim, in “We are committed to transparency with our community while upholding the privacy of victims” we edited to “… upholding the privacy of victims and people who ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. 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 people who report incidents. Our Code of Conduct applies to all people participating in the rOpenSci community, including rOpenSci staff and leadership. It applies to all modes of interaction online including GitHub project repositories, the rOpenSci discussion forum, Slack, ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. 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 for 12 to 14 weeks. Working alongside rOpenSci’s Community Manager, Stefanie Butland, you will use guidelines and checklists to help run some of our established programs like our Blog and Community Calls. Tasks include: Reviewing and editing community-contributed blog posts via Git and GitHub, publishing them to our website, and drafting and ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. 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 lower barriers to working with research data. But it is our community, built on trust, that binds us together and helps us see who we are working for. Many people have submitted their R packages for software peer review (31), reviewed those packages (~60), contributed some code or documentation to ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. rOpenSci HQ Software Peer Review 5 community-contributed packages passed software peer review. baRcodeR – Label Creation for Tracking and Collecting Data from Biological Samples. Author: Yihan Wu; Reviewers: Rayna Harris, Lluís Revilla; Read the Review eia – API Wrapper for ‘US Energy Information Administration’ Open Data. Author: Matthew Leonawicz; Reviewers: David Ranzolin, Philipp Ottolinger; Read the Review mapscanner – R package to print maps, draw on them, and scan them back in. Author: Mark Padgham; Reviewers: Kelly Hondula, Nicholas Potter; Read the Review photosearcher – Searches Flickr for photographs and ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. Testing is a crucial component to any software package. Testing makes surethat your code does what you expect it to do; and importantly, makes it safer to makechanges moving forward because a good test suite will tell you if a change has brokenexisting functionality. Our recent community call on testing is a niceplace to get started with testing. One way to make testing even harder is through including HTTP requests. This addscomplexity for many reasons: Remote resources can change in a variety of ways, all leading to broken tests: Response ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. As of earlier this year, we are now automatically building binaries and pkgdown documentation for all rOpenSci packages. One issue we encountered is that some packages include vignettes that require some special tools/data/credentials, which are unavailable on generic build servers. This post explains how to include such vignettes and articles in your package. On package vignettes By default, R automatically recreates vignettes during R CMD check or when generating pkgdown sites by running all R code. This is useful because it provides some extra testing of your code and ensures ... Read More