Open Tools and R Packages for Open Science

Yanina Bellini Saibene

Alejandra Bellini

Lucio Casalla

Steffi LaZerte

A new post of our interview series “Meeting the stars of the R-universe”. We aim to introduce the teams and people behind the development of software and packages many of us use and which are available through the R-Universe. We want to highlight and explore different teams and projects around the world, the work they do, their processes and users. Our third stop is the

 United States

to talk with members of the PEcAn project.

Meeting the Stars of the R-Universe: PEcAn, an Open Source Project to Take Care of the Planet

Jeroen Ooms

Finding the right tool for the job   The hardest part about effectively using R is finding the best packages for the problem you are trying to solve. I think this is even more important than being fluent in the language itself, which you will pick up along the way as you start using R more frequently. However, building your code on reliable foundations is essential for good results, and difficult to fix later on in a project.

Discovering and learning everything there is to know about R packages using r-universe

Maëlle Salmon

As part of our <a href="/multilingual-publishing/">multilingual publishing project</a>, and with <a href="https://www.r-consortium.org/all-projects/awarded-projects/2022-group-2">funding from the R Consortium</a>, we&rsquo;ve worked on the R package <a href="https://docs.ropensci.org/babeldown/">babeldown</a> for translating Markdown-based content using the DeepL API.In this tech note, we&rsquo;ll show how you can use babeldown to translate a Hugo blog post!

How to Translate a Hugo Blog Post with Babeldown

David Winter

A new version of rentrez, our package for the NCBI’s EUtils API, is makingit’s way around the CRAN mirrors. This release represents a substantialimprovement to rentrez, including a new vignettethat documents the whole package. This posts describes some of the new things in rentrez, and gives us a chanceto thank some of the people that have contributed to this package’s development.

Rentrez 1_0 released

Rich FitzJohn

Matt Pennell

Amy Zanne

Will Cornwell

Science is reportedly in the middle of a reproducibility crisis. Reproducibility seems laudable and is frequently called for (e.g., nature and science). In general the argument is that research that can be independently reproduced is more reliable than research that cannot be independently reproduced.

Reproducible research is still a challenge

Karthik Ram

Our team has been cranking out a large number of tools over the past several months. As regular readers are aware, our software packages provide programmatic access to a diverse and extensive trove of scientific data. More recently we’ve expanded our efforts to build more general purpose and cross-domain tools.

rOpenSci developer meeting in March

Scott Chamberlain

We are building a taxonomic toolbelt for R called taxize - which gives you programmatic access to many sources of taxonomic data on the web. We just pushed a new version to CRAN (v0.1.5) with a lot of changes (see here for a rundown). Here are a few highlights of the changes.

taxize changes

To help you use rOpenSci packages we put tutorials up on our site at /tutorials. Up to now, we created them with combination of raw html + converting code blocks to html and inserting them, etc. – it was a slow process to update them when changes happened in our packages. So we thought of a better plan…  Recently CRAN started accepting R package vignettes (basically, tutorials built in to packages) in R Markdown format.

A new tutorials setup

Apoorv Anand

Bruna Wundervald

Eunseop Kim

Emi Tanaka

François Michonneau

Francisco Cardozo

Erle Holgersen

Marie Vendettuoli

Jonathan Keane

One important aspect of rOpenSci’s mission is to build capacity and promote passionate community members who help the open science and open source software community grow and improve. The rOpenSci Champions Program is a unique opportunity for us to identify, recognize, and reward such individuals and support them in their work to improve their communities and the wider ecosystem.

Introducing rOpenSci Mentors - Cohort 2023-2024

Sayani Gupta

This was how being a newcomer to rOpenSci OzUnconf 2019 felt. It was incredible to be a part of such a diverse, welcoming and inclusive environment. I thought it would be fun to blog about how it all began, and the twists and turns we experienced along the way as we developed the gghdr package. The package provides tools for plotting highest density regions with ggplot2 and was inspired by the package hdrcde developed by Rob J Hyndman.

A Journey to gghdr

The rOpenSci Team

Dear rOpenSci friends, it’s time for our monthly news roundup! You can read this post on our blog.Now let’s dive into the activity at and around rOpenSci! rOpenSci HQ  Meeting the stars of the R-universe: Sébastien Rochette   Knowing our community’s stories helps us to learn about the people behind our software, brings us closer and offers us new opportunities.

rOpenSci News Digest, March 2023

We strive for high quality in our suite of packages, in practice via a system of software peer review, and via packaging guidelines that keep growing. There is therefore a risk of increasing the workload of package authors, who already have a lot on their plate. To avoid that, when explaining how to do things in our dev guide, we recommend existing automated tools to authors.

rodev: helpers for rOpenSci package authors

This week we released version 3.0 of the curl R package to CRAN. You may have never used this package directly, but curl provides the foundation for most HTTP infrastructure in R, including httr, rvest, and all packages that build on it. If R packages need to go online, chances are traffic is going via curl.

Changes to Internet Connectivity in R on Windows

rOpenSci

Stefanie Butland

rOpenSci’s overarching mission is to promote a culture of transparent, open, and reproducible research across various scientific communities. All of our activities are geared towards lowering barriers to participation, and building a community of practitioners around the world.

Announcing our first fellowship awarded to Dr. Nick Golding

Liz Hare

R is a language and environment for statistical computing.There are several tools and approaches for interacting with R, but not all are accessible with screen readers.This guide provides an overview of the tools and techniques available to screen reader users across different operating systems, with practical tips and resources to help them navigate the R environment.This guide may not be complete, but I hope it serves as a valuable starting

Resources For Using R With Screen Readers

Nick Golding

Chris Grieves

Hugo Gruson

Thomas White

Hao Ye

Stefanie Butland,

 rOpenSci Community Manager

Some things are just irresistible to a community manager – PhD student Hugo Gruson’s recent tweets definitely fall into that category.

When Standards Go Wild - Software Review for a Manuscript

Will Landau

The drake R package is not only a reproducible research solution, but also a serious high-performance computing engine. The package website introduces drake, and this technical note draws from the guides on high-performance computing and timing in the drake manual. You can help! Some of these features are brand new, and others are newly refactored.

drake's improved high-performance computing power

The ssh package provides a native ssh client for R. You can connect to a remote server over SSH to transfer files via SCP, setup a secure tunnel, or run a command or script on the host while streaming stdout and stderr directly to the client. The intro vignette provides a brief introduction.

Bugfix release for the ssh package

At rOpenSci we are developing on a suite of packages that expose powerful graphics and imaging libraries in R. Our latest addition is av – a new package for working with audio/video based on the FFmpeg AV libraries. This ambitious new project will become the video counterpart of the magick package which we use for working with images.

The av Package: Production Quality Video in R

Remember our recent post showing that one can wrangle Markdown filesprogrammatically without regex? Thattech note showed how to convert Markdown bodies to XML in order toextract information from them.

tinkr: editing Markdown documents using XML tools

Greg Wilson

Over the past thirty years I have written five technical books,co-written three others,and edited a further six.Since 2007 they have all lived in GitHub repositories,as did the first versions of the Software Carpentry lessons that I helped to write.

Labels For Technical Writing Projects

Vincent van Hees

R packages, like any software, require maintenance. Package maintenance includes: Fixing bugs when discovered. Adapting to updates in package dependencies. Providing some level of user and contributor support. When desired, refactoring code or adding new functionality. Without maintenance efforts a package is at risk of losing its value. Yet, maintaining a package for years or even decades can be challenging as it is time consuming.

My Experience With Long Term Maintenance Of An R Package

Do you maintain an open-source project like an R package or a collection thereof, and wonder how to best use various communication channels to inform and engage with your community of users?We’ve consolidated this list of tips.Some of them are required in our opinion, others are simply nice to have.

Communication Tips for your Open-Source Project

Dear rOpenSci community,  This is a bit of a bittersweet announcement… After nearly 13 years, it’s time for me to step down as the Executive Director of rOpenSci. In the summer of 2011 I co-founded rOpenSci alongside a group of dedicated colleagues. What began as a casual collaboration among open science enthusiasts quickly evolved into something far more meaningful.

From the Founding Director: My Farewell to rOpenSci

Abstract / TLDR   R-universe now provides MacOS arm64 binaries for all R packages.

R-universe now builds MacOS ARM64 binaries for use on Apple Silicon (aka M1/M2/M3) systems

Camille Santistevan

Maya Sanghvi

Lou Woodley

Mauro Lepore

Heather Turner

Pao Corrales

Our first cohort of the rOpenSci Champions Program has now completed the first phase of their training.One of the goals of this program was to ensure that all participants gained new skills and understanding.We wanted to support Champions and Mentors, but also those who applied to the program but were not selected.Therefore we ensured that all groups had access to different training opportunities.

rOpenSci Champions Pilot Year: Training Wrap-Up

Cesar Luis Aybar Camacho

Marc Choisy

We designed the rOpenSci Champions Program with a mentorship aspect. Mentoring plays a significant role in the growth and development of both mentors and mentees alike.

rOpenSci Champions Program Teams: Meet César and Marc

A new post of our interview series “Meeting the stars of the R-universe”. We aim to introduce the teams and people behind the development of software and packages many of us use and which are available through the R-Universe. We want to highlight and explore different teams and projects around the world, the work they do, their processes and users.

Meeting the Stars of the R-Universe: Researching Our Brain with the Magic of the R-Universe

Dear rOpenSci friends, it’s time for our monthly news roundup!  You can read this post on our blog.Now let’s dive into the activity at and around rOpenSci! rOpenSci HQ  One-page HTML package manuals on R-universe!   We have recently started building HTML reference manuals for each package in the R-universe! For packages that have had an update in the past 3 weeks, the reference manual is now linked from the package homepage on R-universe.dev.

rOpenSci News Digest, December 2022

Jeffrey Stevens

The online survey system Qualtrics can be a great way to collect data from research participants, customers, and stakeholders. I use it frequently to conduct research studies with participants or just to poll students and collaborators.

Working with Qualtrics Data - Part 1: Importing Data

Dear rOpenSci friends, it’s time for our monthly news roundup! You can read this post on our blog.Now let’s dive into the activity at and around rOpenSci!

rOpenSci News Digest, April 2022

Following our recent post on “Safeguards and Backups for GitHub Organizations”, nearly one month ago we went one step further and made two-factor authentication (2FA) required for all members and outside collaborators of our main organization, ropensci.It was a timely decision as GitHub since then announced it

 will require all users who contribute code on GitHub.com to enable one or more forms of two-factor authentication (2FA) by the end of

Requiring 2FA for Our Main GitHub Organization

The rOpenSci R-universe is a bit special as, compared to other R-universes, it builds docs for all the packages in our suite.Looking at the dashboard helps us identify failures in building the packages as well as in building the pkgdown websites.We then help authors fix these issues in order to comply with our package curation policy.As a package author you should also rely on continuous integration in your own repo for catching e.g. R CMD check

A Blend of Package Build Failures

As part of rOpenSci’s multilingual publishing project

 1

, we have been developing the babeldown R package, for translating Markdown-based content using the DeepL API.

How to Update a Translation with Babeldown

We are excited to welcome Emily Riederer, Adam Sparks, and Jeff Hollister to our team of Associate Editors for rOpenSci Software Peer Review.They join Laura DeCicco, Julia Gustavsen, Anna Krystalli, Mauro Lepore, Karthik Ram, Noam Ross, Maëlle Salmon, and Melina Vidoni.

Announcing New Software Peer Review Editors: Emily Riederer, Adam Sparks, and Jeff Hollister

Have you ever found a command-line tool that’s perfect for getting your job done, and wanted to use it from an R script or package?E.g. some sort of scientific software providing a specific functionality made available though a command-line interface (CLI)?  In this post, we have a look at a few options for writing such CLI wrappers in R.In particular, we compare the base R functions system() and system2(), the sys package and the processx

How to Use System Commands in your R Script or Package

Nicholas Tierney

We’re excited to announce that we’ll be hosting monthly social coworking + office hours sessions via Zoom, starting September 7th!

rOpenSci Introduces Monthly Social Coworking and Office Hours

Dear rOpenSci friends, it’s time for our monthly news roundup! You can read this post on our blog.Now let’s dive into the activity at and around rOpenSci! rOpenSci HQ  Meeting the stars of the R-universe: PEcAn, an Open Source Project to Take Care of the Planet   Knowing our community’s stories helps us to learn about the people behind our software, brings us closer and offers us new opportunities.

rOpenSci News Digest, June 2023

April Wright

Cristian Román-Palacios

Josef Uyeda

The data.table package enables high-performance extended functionality for data tables in R. treedata.table is a wrapperfor data.table for phylogenetic analyses that matches a phylogeny to the data.table, and preserves matching during data.table operations.Using the data.table package greatly increases analysis reproducibility and the efficiency of data manipulation operations over other ways of performing similar tasks inbase R, enabling

The treedata.table Package

Thanks to a quite overdue update of Hugo on our build system

 1

, 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 code (i.e.

 syntax highlighting

), and accentuate parts of your code (i.e.

 line

Highlights of Hugo Code Highlighting

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.

Thank You, 2019

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 for their contributions to rOpenSci.

2 Months in 2 Minutes - rOpenSci News, December 2019

Vikram B. Baliga

Studies of muscle physiology often rely on closed-source, proprietary software for not only recording data but also for data wrangling and analyses. Although specialized software might be necessary to record data from highly-specialized equipment, data wrangling and analyses should be free from this constraint.

workloopR: Analysis of work loops and other data from muscle physiology experiments in R

Claudia Vitolo

Whether you are an environmental scientist, a pollution expert or just concerned about the air you breathe when cycling in the United Kingdom, the ropensci rdefra package can help find the information you need. This package gives you access to the UK-AIR database, hosted by the Department for Environment, Food &amp;

Get air quality data for the United Kingdom using the rdefra package

If you have an R package on CRAN, you probably know about CRAN checks. Each package on CRAN, that is not archived on CRAN

 1

, has a checks page, like this one for ropenaq:https://cloud.r-project.org/web/checks/check_results_ropenaq.html The table above is results of running R CMD CHECK on the package on a combination of different operating systems, R versions and compilers.

cran checks API: an update

Ambitious workflows in R, such as machine learning analyses, can be difficult to manage. A single round of computation can take several hours to complete, and routine updates to the code and data tend to invalidate hard-earned results. You can enhance the maintainability, hygiene, speed, scale, and reproducibility of such projects with the drake R package.

Community Call - Reproducible Workflows at Scale with drake

The rOpenSci project is a poster child for the fluid collaboration that has become increasingly common these days thanks to platforms like Twitter and GitHub. It has been really inspring to see open discussions take shape as rough ideas, which rapidly turn into prototype research software, all of which are now happening in the order of few days to weeks rather than months to years.

rOpenHack report

Last month we released a new version of pdftools and a new companion package qpdf for working with pdf files in R. This release introduces the ability to perform pdf transformations, such as splitting and combining pages from multiple files. Moreover, the pdf_data() function which was introduced in pdftools 2.0 is now available on all major systems.

Join, split, and compress PDF files with pdftools

You can find members of the rOpenSci team at various meetings and workshops around the world. Come say ‘hi’, learn about how our software packages can enable your research, or about our process for open peer software review and onboarding, how you can get connected with the community or tell us how we can help you do open and reproducible research. Where’s rOpenSci?

Chat with the rOpenSci team at upcoming meetings

Dan Sholler

We tend to know a good open source research software project when we see it: The code is well-documented, users contribute back to the project, the software is licensed and citable, and the community interacts and co-produces in a healthy, productive fashion.

Community Call Follow-up - Governance of Open Source Research Software Organizations

Do you have code that accompanies a research project or manuscript? How do you review and archive that code before you submit a paper? Our next Community Call will present different perspectives on this hot topic, with plenty of time for Q&amp;A. What’s the culture of the group around feedback and code collaboration? What are the use cases? What are some practices that can adopted?

Community Call - Code Review in the Lab, or ... How do you review code that accompanies a research project?

Optical character recognition (OCR) is the process of extracting written or typed text from images such as photos and scanned documents into machine-encoded text. The new rOpenSci package tesseract brings one of the best open-source OCR engines to R. This enables researchers or journalists, for example, to search and analyze vast numbers of documents that are only available in printed form.

The new Tesseract package: High Quality OCR in R

Dear rOpenSci friends, it’s time for our monthly news roundup! You can read this post on our blog.Now let’s dive into the activity at and around rOpenSci! rOpenSci HQ  WIP: WebAssembly support in R-universe! Thanks to some help from George Stagg, we added experimental support for building WebAssembly binary packages. This makes it possible to install packages in webr, directly from the R-universe.

rOpenSci News Digest, September 2023

Dear rOpenSci friends, it’s time for our monthly news roundup! You can read this post on our blog.Now let’s dive into the activity at and around rOpenSci! rOpenSci HQ  rOpenSci in the Research Organization Registry   rOpenSci was added to the Research Organization Registry (ROR) in its latest release. The ROR is a global, community-led registry of open persistent identifiers for research organizations.

rOpenSci News Digest, May 2024

How packages appear in r-universe   Last month we explained how r-universe makes it easy to search and browse through the countless R packages, articles, and datasets to let you discover and learn new things. We are continuously growing this database by adding more R projects, to guide you through everything the R ecosystem has to offer. Currently r-universe is tracking and indexing of over 18.000 R packages.

How r-universe searches for packages on CRAN / Bioconductor

rOpenSci is a nonprofit organization that is funded entirely by grants and donations. These contributions enable us to keep our projects and infrastructure active and accessible to the community. Our projects are dedicated to establishing and upholding both technical and social infrastructure that supports open and reproducible science for all our members.

Empowering Open Science: Donate to Support our Mission

Dear rOpenSci friends, it’s time for our monthly news roundup! You can read this post on our blog.Now let’s dive into the activity at and around rOpenSci! rOpenSci HQ  Reminder about giving season: consider donating to rOpenSci   This Giving Season consider donating to rOpenSci to support our mission of empowering Open Science.

rOpenSci News Digest, December 2023

The R-Universe is used by professionals from different fields, although they all pursue the same objective:

 to offer their R packages in a simple and accessible way

. At rOpenSci we work to provide tools that facilitate access to data and research software generated with good software development practices and in a friendly community.

The rOpenSci Multiverse

Dear rOpenSci friends, it’s time for our monthly news roundup! You can read this post on our blog.Now let’s dive into the activity at and around rOpenSci! rOpenSci HQ R-universe Video and resources from our past community call about

 rOpenSci’s R-universe Project

were posted.

rOpenSci News Digest, June 2021

conditionz is a new (just on CRAN today) R package for controlling how many times conditions are thrown.

conditionz: control how many times conditions are thrown

On June 14 I was invited to present at the CZI Open Science 2024 event. I was asked to participate in “Case Study Session 3: Demonstrating Impact of Open Science” and to explore the challenges of using traditional academic metrics for measuring project impact with an emphasis on alternative approaches. I was very excited to share our experiences and to learn from others projects. Here I present a summary of this talk.

Metrics, Impact and Community Management

Textual data and natural language processing are still a niche domain within the R ecosytstem.

New rOpenSci Packages for Text Processing in R

Dear rOpenSci friends, it’s time for our monthly news roundup! You can read this post on our blog.Now let’s dive into the activity at and around rOpenSci! rOpenSci HQ  Recordings of useR! 2021   Recordings of useR! 2021 are now available on the conference website.

rOpenSci News Digest, August 2021

Dear rOpenSci friends, it’s time for our monthly news roundup! You can read this post on our blog.Now let’s dive into the activity at and around rOpenSci! rOpenSci HQ  R-universe gets advanced search! The landing page for rOpenSci’s R-universe platform has gotten a makeover to facilitate easy searching through thousands of available R packages and articles.

rOpenSci News Digest, March 2022

Diego Hernangómez

When GitHub announced support for CITATION.cfffiles I though ofcreating a package that would assist R developers in this matter. I was alreadyusing codemetar for most of my packages,so I was familiar with the creation of these kind of metadata files.

How I Test cffr on (about) 2,000 Packages using GitHub Actions and R-universe

rOpenSci News Digest, October 2021

Dear rOpenSci friends, it’s time for our monthly news roundup!You can read this post on our blog.Now let’s dive into the activity at and around rOpenSci!

rOpenSci News Digest, April 2021

The R-universe build system   The R-universe system is a complex effort, consisting of numerous frontend and backend pieces that operate across various platforms. A key challenge in developing such a system is managing overall complexity by finding ways to reduce the problem into smaller, loosely coupled components, which can be thought of, and developed, somewhat independently.

A first look at the R-universe build infrastructure

Dennis Irorere

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.

Accessing GraphQL from R

At rOpenSci, we encourage R package developers to take advantage of Continuous Integration services to automatically check the package on different platforms, with different versions of R. The rOpenSci dev guide dedicates chapter 2 to the topic of

 Continuous Integration Best Practices

, and recommends a few common CI vendors, including Travis CI. Travis CI has been a pioneer in free public CI services, and made the concept popular in

Moving away from Travis CI

There is an increasing set of R packages for interacting with the web from R, whether it be the low level tools to interact with the web via http (see RCurl and httr), parsing data from the web (like RJSONIO and XML), or wrappers to web APIs that provide data (like twitteR).  Most of you probably know about CRAN Task Views that aggregate information about R packages and functions on a particular subject area into a simple web page.

A task view for interacting with the web from R

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 a table of &gt; 100 rOpenSci packages for access to open data.

2 Months in 2 Minutes - rOpenSci News, June 2020

The goal of the rOpenSci Champions Program is to enable more members of historically excluded groups to participate in, benefit from, and become leaders in the R, research software engineering, and open source and open science communities. This program includes 1-on-1 mentoring for the Champions as they complete a project and perform outreach activities in their local communities.

Fostering Equity and Leadership: the rOpenSci Champions Program Selection Process

A number of the APIs we interact with (e.g., PLOS full text API, and USGS’s BISON API in rplos and rbison, respectively) expose Solr endpoints. Solr is an Apache hosted project - it is a powerful search server.

rOpenSci - open tools for open science

UCSCXenaTools: Retrieve Gene Expression and Clinical Information from UCSC Xena for Survival Analysis

restez: Query GenBank locally