Open Tools and R Packages for Open Science

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  🔗rOpenSci 2024 Highlights and what comes next in 2025  In this blog post, the rOpenSci Team shares the highlights of 2024 and what come next in 2025.

rOpenSci News Digest, January 2025

We’re very excited to introduce the new rOpenSci Champions! This cohort will participate in the program and carry out their work in Spanish, allowing us to continue strengthening the open science and research software development community in this language. We’re excited about the projects they’ll be developing, which tackle real-world challenges across diverse disciplines and regions of Latin America.

Open Science with a Latin American Identity: Meet the New Cohort of the rOpenSci Champions Program

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, October 2024

We recently introduced a new paragraph to the development version of our dev guide This complements the statistical software review requirement for Bayesian software. This tech note’s aim is to make the new requirement louder, demonstrate some approaches to verbosity control, and to gather community feedback!

Please Shut Up! Verbosity Control in Packages

The NumFOCUS Diversity &amp; Inclusion in Scientific Computing (“DISC”) Unconf took place as a hybrid event in São Paulo, Brazil, from March 14 to 16, 2025.Our community manager, Yanina Bellini Saibene, and rOpenSci Champions, Andrea Gomez Vargas and Liz Hare, participated.In this short post we report on our experience at and around the unconference.

rOpenSci Participation at NumFOCUS’ DISC Unconf

rOpenSci is one of the first organizations in the R community I ever interacted with, when I participated in the 2016 rOpenSci unconf. I have since reviewed several rOpenSci packages and been so happy to be connected to this community, but I have never submitted or maintained a package myself. All that changed when I heard the call for a new maintainer for the qualtRics package. “IT’S GO TIME,” I thought.

Relaunching the qualtRics package

Phylogenetic trees are commonly used to present evolutionary relationships of species. Newick is the

 de facto

format in phylogenetic for representing tree(s). Nexus format incorporates Newick tree text with related information organized into separated units known as blocks. For the R community, we have ape and phylobase packages to import trees from Newick and Nexus formats.

treeio: Phylogenetic data integration

🔗webmockr  webmockr is an R library for stubbing and setting expectations on HTTP requests.It is a port of the Ruby gem webmock. webmockr works by plugging in to another R package that does HTTP requests. It currently only works with crul right now, but we plan to add support for curl and httr later.

webmockr: mock HTTP requests

Jonathan Keane

This post describes a few different aspects behind the scenes of the development of dittodb which recently went through the rOpenSci peer review process and was released to CRAN on 24 July 2020.This isn’t an introduction to the package itself (that’s available on dittodb’s site), but rather a look behind the scenes of the conceiving of the idea, the inspiration for, some of the development of, and history behind dittodb.

Developing dittodb

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

We have great news: The call for applications to be part of the new cohort of our 2025 Program is now open! And for the first time it will be in Spanish! Our program seeks to identify, recognize and reward people who are leaders in an open science community, research software engineering and the R programming community. This year’s program is focused on people from Latin America and for the first time will be conducted entirely in Spanish.

rOpenSci Champions Program 2025: In Spanish!

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  🔗Open Science and Open Source only with Diversity, Equity, Inclusion, and Accessibility  Including all of humanity is and always will be at the heart of open science.Read more about our mission in our blog post.

rOpenSci News Digest, February 2025

We are excited to announce that R-Universehas been named the R Consortium’s newest Top-Level Project!

R-Universe Named an R Consortium Top-Level Project

Do you remember your first contribution to open source?Or are you still waiting to make it? Contributing to open source can be very rewarding, but also incredibly intimidating.When we asked about first time contributions on the rOpenSci Slack,people recalled the challenges and mistakes they made, but mostly how much they learned from and enjoyed that experience.For open source maintainers, contributions can also lead to mixed feelings,as

Looking for Maintainers to Support First-Time Contributors

Recently Yanina Bellini Saibene reminded usto update our Slack profile: After doing that I went on to updating my profile photos on the rOpenSciwebsite, which ended up teaching me a few git tricks I would like to share here.Thanks Maëlle Salmon for the encouragement, andSteffi LaZerte for reviewing this post.

Git Tricks for Working with Large Repositories

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

We are excited to announce that R-Universe has been awarded a Google Season of Docs grant. R-Universe is rOpenSci’s platform for testing, building, distributing, and discovering R packages, led by Jeroen Ooms.

R-Universe Documentation Gets a Boost from Google Season of Docs

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 potentialviolations of our Code.

rOpenSci 2022 Code of Conduct Transparency Report

🔗Introduction  When I was in grad school at Emory, I had a favorite desk in the library. The desk wasn’t particularly cozy or private, but what it lacked in comfort it made up for in real estate. My books and I needed room to operate. Students of the ancient world require many tools, and when jumping between commentaries, lexicons, and interlinears, additional clutter is additional “friction”, i.e., lapses in thought due to frustration.

Exploratory Data Analysis of Ancient Texts with rperseus

rOpenSci

I’ve raved about the value of extending a personalized welcome to new community members and I recently shared six tips for running a successful hackathon-flavoured unconference. Building on these, I’d like to share the specific approach and (free!) tools I used to help prepare new rOpenSci community members to be productive at our unconference.

The Value of Welcome, part 2: How to prepare 40 new community members for an unconference

Our community is our best asset. It’s so important to us, it’s in our mission statement. We recognize that communities are not inclusive by default; they require deliberate attention, including an enforceable Code of Conduct. rOpenSci is committed to providing a safe, inclusive, welcoming, and harassment-free experience for everyone.

rOpenSci Code of Conduct Annual Review

Make

 1

-like pipelines enhance the integrity, transparency, shelf life, efficiency, and scale of large analysis projects.With pipelines, data science feels smoother and more rewarding, and the results are worthy of more trust.

 targets

install.packages("targets") The targets

 2

package is a new pipeline toolkit for R.It recently cleared software review, and it is now on CRAN.

targets: Democratizing Reproducible Analysis Pipelines

More and more R packages access resources on the web, and play crucial roles in workflows.Examples from the rOpenSci suite of packages include rromeo, GSODR, qualtRics, rnassqs, and many, many others.Like for all other packages, appropriate unit testing can make them more robust.However, unit testing of these packages can bring special challenges: dependence of tests on a good internet connection, testing in the absence of authentication

Learn All About HTTP Testing: Book Update

In 2024, we remained committed to open science and open source software.We continued to build a welcoming andinclusive community, through innovation and collaboration. Here are the highlights of the year: 🔗R-Universe  R-Universe, rOpenSci’s platform for finding and publishing R packages,saw major advancements in 2024,making it an increasingly useful and trusted resource for the wider R community.

rOpenSci 2024 Highlights

Scott Chamberlain

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.

fulltext: Behind the Scenes

Stefanie Butland

🔗rOpenSci HQ  🔗rOpenSci at R-Ladies  Our community manager Stefanie Butland, and one of our software review editors Brooke Anderson, are speaking remotely at an R-Ladies East Lansing meetup Thursday, October 22nd. They will talk about our how to get involved in rOpenSci using our new Contributing Guide as an entry point, and through participating in software review as a package author or reviewer.

2 Months in 2 Minutes - rOpenSci News, October 2020

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

Zhang-He Goh

Jonny Coates

Hugo Gruson

At the eLife Sprint in September 2020, we revamped the covidpreprints.com website, which aims at featuring landmark preprints on a timeline of the pandemic. 🔗The birth of the project  The ongoing COVID-19 pandemic has led to about 35 million confirmed cases and over a million deaths worldwide.

Covidpreprints.com: Automating Website Updates with the europepmc and rAltmetric Packages

Karthik Ram

UPDATE: mapping functions are in a separate package now (mapr). Examples that do mapping below have been updated. The rOpenSci projects aims to provide programmatic access to scientific data repositories on the web. A vast majority of the packages in our current suite retrieve some form of biodiversity or taxonomic data.

Species occurrence data

Julia Stewart Lowndes

At their closing keynote at the 2020 RStudio Conference, Hilary Parker and Roger Peng mentioned that they hatched the idea for their excellent Not So Standard Deviations podcast following their reunion at the 2015 rOpenSci unconf, (“runconf15”). That statement went straight to my heart because it pin-pointed how I had been feeling throughout the week of RStudio Conference that I had been unable to name.

rOpenSci's Leadership in #rstats Culture

parzer is a new package for handling messy geographic coordinates.The first version is now on CRAN, with binaries coming soon hopefully (seenote about installation below). The package recently completed rOpenScireview. 🔗parzer motivation  The idea for this package started with a tweet from Noam Ross(https://twitter.com/noamross/status/1070733367522590721) about 15 months ago.

parzer: Parse Messy Geographic Coordinates

We’re thrilled to be introducing a new member of our team. Mark Padgham has joined rOpenSci as a Software Research Scientist working full-time from Münster, Germany. Mark will play a key role in research and development of statistical software standards and expanding our efforts in software peer review, enabled by new funding from the Sloan Foundation.

Introducing Mark Padgham, rOpenSci’s new Software Research Scientist

Today we are pleased to announce that we have received new funding from the Gordon and Betty Moore Foundation. The $894k grant will help us improve infrastructure for R packages and enable us to move towards a

 science first

package ecosystem for the R community. You may have already noticed some developments on this front when we announced our automated documentation server back in June.

rOpenSci Announces a New Award From The Gordon and Betty Moore Foundation to Improve the Scientific Package Ecosystem for R

We’re delighted to announce that we have received new funding from the Alfred P. Sloan Foundation. The $678K grant, awarded through the Foundation’s Data &amp; Computational Research program, will be used to expand our efforts in software peer review.

rOpenSci Announces $678K Award from the Sloan Foundation to Expand Software Peer Review

Are you passionate about statistical methods and software? If so we would love for you to join our team to dig deep into the world of statistical software packages. You’ll develop standards for evaluating and reviewing statistical tools, publish, and work closely with an international team of experts to set up a new software review system.

rOpenSci Hiring for New Position in Statistical Software Testing and Peer Review

Our 1-hour Call on Reproducible Research with R will include three speakers and 20 minutes for Q &amp; A.

 Ben Marwick

will introduce you to a research compendium, which accompanies, enhances, or is a scientific publication providing data, code, and documentation for reproducing a scientific workflow.

Community Call - Reproducible Research with R

At rOpenSci, our mission is to and we achieve this through We feel it is a time  to reiterate and clarify why this is and what it means. The open in open source and open science means more than how we share code or data.It means knocking down the barriers to participation so that it is open and accessible to all,that everyone can join in the benefits and joys of science, and removing our blinders to the humanity of those we previously missed.

Open Science and Open Source only with Diversity, Equity, Inclusion, and Accessibility

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  🔗Community call recording: Navigating the R ecosystem using R-universe  Video and resources. Learn more about R-Universe and how you can use it to improve your R package development workflow.

rOpenSci News Digest, September 2024

🔗Introduction  ramlegacy is a new R package to download, cache and read in all the different versions of the  RAM Legacy Stock Assessment Database, a public database containing stock assessment results of commercially exploited marine populations from around the world.

ramlegacy: a package for RAM Legacy Database

I am pleased, excited, and humbled to announce that I am stepping into the role of Executive Director of rOpenSci starting April 1. First, let me give my gratitude to our outgoing Executive Director and friend Karthik Ram for his leadership and mentorship running rOpenSci the past decade. He’s been a steady hand and visionary that helped our community accomplish so much together in this time.

Hello from our New Executive Director!

This week version 2.0 of the V8 package has been released to CRAN. Go get it now!install.packages("V8") The V8 package provides an embedded JavaScript engine that can be used inside of R. You can use it interactively as a JavaScript console, but it is mostly useful for wrapping JavaScript libraries in R packages. Some cool examples include jsonld, jsonvalidate, and daff.

A Major Upgrade of the V8 package

There seem to be a lot of ways to write about your R package, and rather than haveto decide on what to focus on I thought I’d write a little bit about everything.To begin with I thought it best to describe what problem rdhs tries to solve,why it was developed and how I came to be involved in this project.

Interacting with The Demographic and Health Surveys (DHS) Program data

The package targets maintained by Will Landau, and its companion packages, are pipeline tools, that coordinate the pieces of computationally demanding analysis projects. 🔗Help sustain targets discussion forums!

Help users and developers of targets by answering questions!

The package assertr maintained by Tony Fischetti, provides functionality to assert conditions that have to be met so that errors in data used in analysis pipelines can fail quickly.The provided functionality is similar to stopifnot() but more powerful, friendly, and easier for use in pipelines. 🔗Contributed to assertr!

Help make assertr better! Come close issues

🔗The Ecology Hackathon  Almost one year ago now, ecologists filled a room for the “Ecology Hackathon: Developing R Packages for Accessing, Synthesizing and Analyzing Ecological Data” that was co-organised by rOpenSci Fellow, Nick Golding and Methods in Ecology and Evolution. This hackathon was part of the “Ecology Across Borders” Joint Annual Meeting 2017 of BES, GfÖ, NecoV, and EEF in Ghent.

rcites - The story behind the package

We’ve just released a new version of rnoaa with A LOT of changes. Check outthe release notesfor a complete list of changes.

rnoaa: new data sources and NCDC units

pubchunks is a package grown out of the fulltext package. fulltextprovides a single interface to many sources of full text scholarly articles. Aspart of the user flow in fulltext there is an extraction step where fulltext::chunks()pulls parts of articles out of XML format article files.

pubchunks: extract parts of scholarly XML articles

In late November 2018, we ran the third annual rOpenSci ozunconf. This is the sibling rOpenSci unconference, held in Australia. We ran the first ozunconf in Brisbane in 2016, and the second in Melbourne in 2017.

 Photos taken by Ajay from Fotoholics

As usual, before the unconf, we started discussion on GitHub issue threads,and the excitement was building with the number of issues.

Continuing to Grow Community Together at ozunconf, 2018

Last week Google and friends released the new major version of their OCR system: Tesseract 4. This release builds upon 2+ years of hard work and has completely overhauled the internal OCR engine. From the tesseract wiki: We have now also updated the R package tesseract to ship with the new Tesseract 4 on MacOS and Windows. It uses the new engine by default, and the results are extremely impressive!

Tesseract 4 is here! State of the art OCR in R!

rgbif was seven years old yesterday! 🔗What is rgbif? rgbif gives you access to data from the Global Biodiversity Information Facility (GBIF) via their API.

rgbif: seven years of GBIF in R

A while ago weonboarded anexciting package, codemetarby Carl Boettiger. codemetar is an R specificinformation collector and parser for the CodeMetaproject. In particular, codemetar candigest metadata about an R package in order to fill the termsrecognized by CodeMeta. This meansextracting information from DESCRIPTION but also from e.g. continuousintegration

 1

badges in the README!

All the Badges One Can Earn: Parsing Badges of CRAN Packages READMEs

eBird is an online tool for recording birdobservations. The eBird database currently contains over 500 millionrecords of bird sightings, spanning every country and nearly every birdspecies, making it an extremely valuable resource for bird research andconservation. These data can be used to map the distribution andabundance of species, and assess how species’ ranges are changing overtime. This dataset is available for download as a text file;

Extracting and Processing eBird Data

Being a part of the rOpenSci Champion’s program has been a transformative experience, pushing me to explore the world of R package development and contribute to the world of open science. While my initial project proposal took a different route, the unexpected journey led me to create a valuable tool that I am proud to call my own – an R package ChartkickR.

2023 rOpensci Champions Program: My Experience

Have you ever needed to connect to a remote server over SSH to transfer files via SCP or to setup a secure tunnel, and wished you could do so from R itself? The new rOpenSci ssh package provides a native ssh client in R allows you to do that and even more, like running a command or script on the host while streaming stdout and stderr directly to the client.

The ssh Package: Secure Shell (SSH) Client for R

After Stefanie’s recap of unconf18, this week the blog will feature brief summaries of projects developed at the event: each day 4 to 5 projects will be highlighted. (Full set of project recaps: recap 1, recap 2, recap 3, recap 4) In the following weeks, a handful of groups will share more thorough posts about their work.

Unconf18 projects 1: mchtoolbox, pkginspector, dataspice, rOpenSciEd, rOpenInterviews

As part of our multilingual publishing project, and with funding from the R Consortium, we’ve worked on the R package babeldown for translating Markdown-based content using the DeepL API.In this tech note, we’ll show how you can use babeldown to translate a Hugo blog post!

How to Translate a Hugo Blog Post with Babeldown

On March the 17th I had the honor to give a keynote talk about rOpenSci’s package onboarding system at the satRday conference in Cape Town, entitled “Our package reviews in review: introducing and analyzing rOpenSci onboarding system”. You can watch its recording, skim through the corresponding slides or… read this series! 🔗What is rOpenSci onboarding?

Our package reviews in review: Introducing a 3-post series about software onboarding data

Our onboarding process, thatensures that packages contributed by the community undergo atransparent, constructive, non adversarial and open review process,involves a lot of work from many actors: authors, reviewers and editors;but

 how much work

? Managing the effort involved in the peer-reviewprocess is a major part of ensuring its sustainability and quality.

How much work is onboarding?

The Pandoc CLI by John MacFarlane is a really useful tool: for instance, rOpenSci community manager Yanina Bellini Saibene recently asked Maëlle whether she could convert a Google Document into a Quarto book.Maëlle solved the request with a combination of Pandoc (conversion from docx to HTML then to Markdown through pandoc::pandoc_convert()) and XPath.You can find the resulting experimental package quartificate on GitHub.Pandoc is not only

Troubleshooting Pandoc Problems as an R User

Just last week we organised the 2nd rOpenSci ozunconference, the sibling rOpenSci unconference, held in Australia. Last year it was held in Brisbane, this time around, the ozunconf was hosted in Melbourne, from October 26-27, 2017. At the ozunconf, we brought together 45 R-software users and developers, scientists, and open data enthusiasts from academia, industry, government, and non-profits.

Building Communities Together at ozunconf, 2017

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 improvements!

rOpenSci News Digest, February 2023

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

I really enjoy using targets for all of my data analysis projects, especially because it helps me structure all of the projects nicely in the same folder.For targets projects, I often produce several figures using ggplot2.However, there are no formal recommendations for saving ggplot2 objects (as opposed to static images) in a targets workflow.

How to Save ggplot2 Plots in a targets Workflow?

🔗Introduction  Panel data contains measurements from multiple subjects measured over multiple time points.Such data can be encountered in many social science applications such as when analysing register data or cohort studies (for example).Often the aim is to perform causal inference based on such observational data (instead of randomized control trials). A new rOpensci-reviewed R package dynamite available on CRAN implements a new class of

Dynamite for Causal Inference from Panel Data using Dynamic Multivariate Panel Models

🔗Two new packages! We released two new packages that we are using in r-universe to render package documentation: postdoc and prismjs. The goal of postdoc is very simple: generate beautiful single-page package manuals in HTML format. Postdoc uses our prismjs and katex packages for server-side highlighting and math.

postdoc 1.0: minimal and uncluttered HTML package manuals

This is the first post of our interview series

 “Meeting the stars of the R-universe”

. We aim to introduce the working groups 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: R Community, Exchange and Learn

🔗Why a Champions Program? Champion programs are designed to identify, recognize, and reward passionate community members. At rOpenSci, we recognize that there is a dismaying lack of diversity in the ecosystem of research software and open source communities. The R Community is no exception; its developers are overwhelmingly white, male, and from a handful of countries.

Announcing the rOpenSci Champions Program!

A growing community of scientists from a variety of disciplines is moving the norms of scientific research toward open practices. Supporters of open science hope to increase the quality and efficiency of research by enabling the widespread sharing of datasets, research software source code, publications, and other processes and products of research.

Governance, Engagement, and Resistance in the Open Science Movement: A Comparative Study

Mentoring is at the heart of what makes rOpenSci a community.Our members mentoring each other at different moments:when someone new joins and needs help navigating the community;when a member steps into a new role, like a reviewer for our software peer review,or project, like become the maintainer of a package, and could use some guidance;during everyday interactions, where people share tips and advise with each other;when someone shares an idea

Supporting rOpenSci Mentors with Practical Tools

Say you have a bug report or feature request to make to a package.How can you use information on GitHub to manage your expectations (will there be a quick fix) and actions (should you go ahead and fork the repository)?In this post, we shall go over sources of information and explain how they can be used.In the end, there is no magical recipe, except perhaps graciousness, as software is made by humans.

Evaluating GitHub Activity for Contributors

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  🔗Help us translate our dev guide to Portuguese  Since last year we started the translation and localization of our Spanish version of our comprehensive guide to software development.

rOpenSci News Digest, October 2023

Do you have an account on the rOpenSci forum?As underlined in our contributing guide, our forum is where we encourage

 Q&amp;A and exploration of ideas on a various range of topics

.Compared to our Slack semi-open workspace, the forum is

 entirely open and much easier to search

, so a great place to gather some collaborative knowledge!We have recently

 streamlined categories

so that it might be

Gather on the rOpenSci Forum

🔗R-universe now has search! We made a series of structural improvements in r-universe to make it easier to browse and discover interesting R packages and articles. Most notably, the r-universe.dev landing page has been overhauled: you can now search directly for any name or keyword across the entire ecosystem:  The homepage also lists the popular topics and organizations, and links to recently active packages, articles, and maintainers.

Searching and browsing the R universe

Are you putting together your useR!2021 conference schedule this weekend? Four rOpenSci staff and lots of community members are giving presentations and there’s something for everyone! 🔗Talks by rOpenSci staff

 Jeroen Ooms

, Lead Infrastructure Engineer, will give a

 keynote talk

about

 the R-universe project

on Friday, July 9, 12:30PM - 1:30PM UTC / 5:30AM PDT.

rOpenSci at useR!2021 - Presentations from Staff and Community

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

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  🔗Open Call for rOpenSci Champions Program Applications!

rOpenSci News Digest, August 2023

Like every R user who uses summary statistics (so, everyone), our team has to rely on some combination of summary functions beyond summary() and str(). But we found them all lacking in some way because they can be generic, they don’t always provide easy-to-operate-on data structures, and they are not pipeable. What we wanted was a frictionless approach for quickly skimming useful and tidy summary statistics as part of a pipeline.

skimr for useful and tidy summary statistics

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

Before everybody made their way to the unconf via LAX and Lyft, attendees discussed potential project ideas online. The

 packagemetrics

package was our answer to two related issues. The first proposal centered on creating and formatting tables in a reproducible workflow.

packagemetrics - Helping you choose a package since runconf17

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.

Introducing BaseSet for mathematical sets

On 21-22 April, the London School of Economics hosted the

 Text Analysis Package Developers’ Workshop

, a two-day event held in London that brought together developers of R packages for working with text and text-related data.

Text Analysis R Developers' Workshop 2017

There’s a lot of work that goes in to making software: the code that does the thing itself, unit testing, examples, tutorials, documentation, and support. rOpenSci software is created and maintained both by our staff and by our (awesome) community. In keeping with our aim to build capacity of software users and developers, three interns from our academic home at UC Berkeley are now working with us as well.

Welcome to our rOpenSci Interns

There is no problem in science quite as frustrating as

 other peoples’ data

. Whether it’s malformed spreadsheets, disorganized documents, proprietary file formats, data without metadata, or any other data scenario created by someone else, scientists have taken to Twitter to complain about it. As a political scientist who regularly encounters so-called “open data” in PDFs, this problem is particularly irritating.

Release 'open' data from their PDF prisons using tabulizer

rOpenSci News Digest, June 2024

The rOpenSci project is 100% supported by grants and donations. If you’re giving this season, please consider donating to rOpenSci. Your donations allow us to support internships, contractors, web services, and community events. We foster a culture that values open and reproducible research using shared data and reusable software.

Donate to rOpenSci this Giving Season

Jeroen Ooms

This week the folks at Github have open sourced their fork of libcmark (based on the extensive PR by Mathieu Duponchelle), which they use to render markdown text within documents, issues, comments and anything else on the Github website.

High Performance CommonMark and Github Markdown Rendering in R

In order to facilitate a transformation towards open and reproducible research, rOpenSci is building and improving not only the technical infrastructure, but the social infrastructure as well. To support this, occasionally a Community Call will focus on a topic that reflects the values of rOpenSci.

Community Call v12 - How do I create a code of conduct for my event/lab/codebase?

A new package isdparser ison CRAN. isdparser was in part liberated from rnoaa,then improved. We’ll use isdparser in rnoaa soon. isdparser does not download files for you from NOAA’s ftp servers. Thepackage focuses on parsing the files, which are variable length ASCII stringsstored line by line, where each line has some mandatory data, and any amountof optional data.

Parse NOAA Integrated Surface Data Files

The new magick package is an ambitious effort to modernize and simplify high-quality image processing in R. It wraps the ImageMagick STL which is perhaps the most comprehensive open-source image processing library available today. The ImageMagick library has an overwhelming amount of functionality. The current version of Magick exposes a decent chunk of it, but being a first release, documentation is still sparse.

Advanced Image-Processing in R with Magick, Part I

Travis is a continuous integration service which allows for running automated testing code everytime you push to GitHub. Hadley’s book about R packages explains how and why R package authors should take advantage of this in their development process.

Testing packages with R Travis for OS-X

The package waywiser maintained by Mike Mahoney provides ergonomic methods for assessing spatial models.Assessing predictive models of spatial data can be challenging,both because these models are typically built for extrapolating outside the original region represented by training data and due to potential spatially structured errors,with “hot spots” of higher than expected error clustered geographically due to spatial structure in the

Help make waywiser better! User requests wanted

The rOpenSci Champions Program starts this 2024 with a new cohort of Champions. We are pleased to introduce you to our Champions and their projects! 🔗Ezekiel Adebayo Ogundepo  Hello, I’m Ezekiel, a data science professional deeply fascinated by the intersection of mathematics, statistics, and real-world challenges.

Introducing rOpenSci Champions - Cohort 2023-2024

rOpenSci News Digest, July 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  🔗Giving season: consider donating to rOpenSci  This Giving Season consider donating to rOpenSci to support our mission of empowering Open Science.

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