Author: rOpenSci - open tools for open science

Feed: R-bloggers. Author: rOpenSci - open tools for open science. Many people in our community actively contribute to rOpenSci projects. Many others would like to contribute but aren’t sure how to go about it. Wanting to get involved in rOpenSci or “give back to open source” means different things to different people. Ideally, a person should be able to find a way to contribute that meets their needs and fits our mission. We created the rOpenSci Community Contributing Guide to make finding paths to contributing more transparent and sustainable. Cover illustration by Lydia Hill We welcome contributors from a continuum ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. In this post I will explain the history behind BaseSet then a brief introduction to sets, followed by showing what you can do with BaseSet. Brief BaseSet history I study diseases to try to find what causes them at a research institute associated with an hospital. Thanks to recent technological advances we can analyze many things from a single patient’s sample. Having so much information available can be overwhelming, making it difficult to find the causes of diseases (but it is much better than not having enough information!). In order ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. The rOpenSci community is supported by our Code of Conduct with a clear description of unacceptable behaviors, instructions on how to make a report, and information on how reports are handled. We, the Code of Conduct Committee, are responsible for receiving, investigating, deciding, enforcing and reporting on all reports of potential violations of our Code. We are committed to transparency with our community while upholding the privacy of victims and people who report incidents. In 2020, we did not receive any Code of Conduct incident reports. We acknowledge that a ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. Science craft As a field linguist, I have spent a lot of time working in villages in the Caucasus, collecting audio from speakers of indigenous languages. The processing of such data involves a lot of time-consuming tasks, so during my field trips I created my own pipeline for data collection. I wrote a number of scripts using different programming languages for automatic renaming, merging, and preannotation of files, making backups, visualizing some data, etc. My method consisted of a combination of solutions developed on the fly to solve specific, independent ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. A new version of vcr was just released. See the release notes for all the details. I want to highlight a few of the more notable changes. New contributor vcr has a new author: Maëlle Salmon. She has been contributing to the package quite a lot lately, including many documentation improvements and big updates to the HTTP Testing in R which covers vcr in addition to some other packages. New serializer vcr now has two serializer options: YAML (which we had before) and JSON (the new one). Serializing here refers ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. rOpenSci HQ We’re thrilled to announce three new rOpenSci Software Review Editors: Laura DeCicco, Julia Gustavsen, and Mauro Lepore and we released the fifth version (v0.5) of the rOpenSci Developer Guide. Our Community Call on The Wild World of Data Repositories took place Dec 16 with an audience of 153 people! The video will be posted, along with collaborative notes and resources, by Dec 21. Software Peer Review 2 community-contributed packages passed software peer review. 6 packages have been submitted for review. We will not be accepting new submissions during ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. Introduction Few months ago, I embarked on a full stack spatial data project at work. The project kicked off amazingly, until I was almost backed to the wall when I discovered that some of the data sources were served via a GraphQL API. Before now, I haven’t worked with GraphQL. But, I have heard a lot about it and how amazing it is for querying data. GraphQL is a query language for application programming interfaces (APIs) that prioritizes giving clients exactly the data they request. It’s designed to make APIs ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. With this blog post, I show how to use the mcbette R package in an informal way. A more formal introduction on mcbette can be found in the Journal of Open Source Science . After introducing a concrete problem, I will show how mcbette can be used to solve it. After discussing mcbette, I will conclude with why I think rOpenSci is important and how enjoyable my experiences have been so far. The problem Imagine you are a field biologist. All around the world, you captured multiple bird species of ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. How to join this free online event with Kara Woo, Daniella Lowenberg, Matt Jones, Carl Boettiger and Karthik Ram. There is no one-size-fits-all protocol for depositing your research data into a public repository in a way that maximizes its reuse and citation. We’ve assembled a panel that will help you understand the issues and opportunities for developing new tools and documentation. This 1-hour event, moderated by Kara Woo, includes 5 speakers and 20 minutes for Q & A on: Where and how to deposit data (or data + software!) Challenges ... Read More

Feed: R-bloggers. Author: rOpenSci - open tools for open science. fulltext is a package I maintain for text-mining the scholarly literature (package docs). You can search for articles, fetch article metadata and abstracts, and fetch full text of some articles. Text-mining the scholarly literature is a research tool used across disciplines. Full text of articles (entire article, not just the abstract) is the gold standard in text-mining in most cases. Over the past years the fulltext package has evolved under the hood in its approach to attempting to get full text articles for its users. The following is a walk ... Read More