Open Tools and R Packages for Open Science

This summer I had a wonderful time attending the Society for Canadian Ornithologists meeting in Saskatoon, Canada.It was super exciting to run into Sunny Tseng, rOpenSci Champion and fellow ornithologist!It’s not often that I am able to run into both types of colleagues (R developers and ornithologists) at the same conference, so I cherish these experiences.

A Gentle Introduction to Open Science

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

The “Climate Sensitive Infectious Disease” (CSID) Network looks to connect a global community of actors contributing towards impactful CSID software tools and establish localized CSID communities that can link existing on-the-ground issues and initiatives to the development and maintenance of CSID tools.

Exploring Open Science, R Packages, and Research Software Development at the CSIDNet AGM 2025

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  🔗Help us maintain {pkgcheck}!  You might know of our {pkgcheck} system used for our automated package checks, and for your own stand-alone and GitHub-action usage on any package. We are seeking co-maintainers for the {pkgcheck} package which powers this system.

rOpenSci News Digest, May 2025

🔗How it started  My journey in creating my first R package all started when I received an email from a colleague who was working with archived soil samples that were collected prior to the advent of GPS technology.These samples were georeferenced using the Manitoba Original Survey Legal Descriptions, which originate from the Dominion Land Survey system, introduced in the late 19th century to organize the European settlement and colonization of

Software Review, Perspectives from an Academic

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

In June 2022 I (Yani) become the rOpenSci Community Manager. To do a good job in this kind of role it is essential to know your community, so as soon I started I dug in: reading our documentation, learning our processes and their metrics, and conducting interviews with team-mates and community members.

rOpenSci Community Collaboration Insight Using Social Networks Analysis

Exciting News!

The Chan Zuckerberg Initiative has awarded rOpenSci a new grant to foster sustainable scientific software as a pillar of Open Science in Latin America by building capacity and community. With this $340K grant, we’re planning to launch a Spanish-language version of our Champions Program, along with other new initiatives to make sustainable software development more accessible to researchers across the region.

Fostering Open Science in Latin America: CZI Awards Funds for Sustainable Research Software Development

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

rOpenSci Software Peer Review’s guidance is gathered in an online book that keeps improving!This blog post summarises what’s new in our Dev Guide 0.9.0, with all changes listed in the changelog. 🔗Now available in Spanish!

rOpenSci Dev Guide 0.9.0: Multilingual Now! And Better

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 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

🔗Introducing cran.dev shortlinks! On r-universe you can find package repositories from many different organizations and maintainers. But sometimes you just want to lookup a particular CRAN package, without knowing the developer.The new cran.dev shortlink service lets you navigate or link directly to the r-universe homepage and docs of any established CRAN package.

New cran.dev shortlinks to package information and documentation

We are pleased to open the call for the second cohort of

 Champions and Mentors

for the rOpenSci Champions Program 🎉 ! This program will continue to support our goal of identifying, recognizing, and rewarding passionate community members who help the community grow and improve.

Open Call for rOpenSci Champions Program Applications!

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: Athanasia Monika Mowinckel  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, April 2023

🔗Downloading repository snapshots  The new snapshot API lets you download a full copy of any CRAN-like repository on r-universe. You can use such a snapshot to mirror the entire CRAN-like repository on your own servers, or for example to build a stable, validated release of your package suite. The API endpoint is simply /api/snapshot and has several options to filter content.

Downloading snapshots and creating stable R packages repositories using r-universe

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 Haydée Svab and Beatriz Milz

It was 2015, a Political Science master’s student had to process data to hand in his thesis and decided to take the opportunity to learn how to use R. To the long and winding road of the academic requirement was added an extra degree of difficulty: incorporating programming software from scratch, with a somewhat steep learning curve.

Divide and Conquer: From polar To the Polarverse

Are you the mother goat or the wolf?Consumers of your online content might care!Be it on social media or other platforms, your profile can sometimes be “verified”.What does it mean? How does one get a green checkmark where it matters?Here’s a primer on domain verification.

A Primer on Domain Verification

A new version of the ropensci magick package has been released to CRAN. Magick is a package for Advanced Image-Processing in R. It wraps the ImageMagick STL which is perhaps the most comprehensive open-source image processing library available today. Our original announcement has more details. New features   This new version now includes a beautiful vignette which gives an overview of the main functionality to get you started!

New in Magick 0.3

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!

R has a reputation of not playing nice on the web. At rOpenSci, we write R pacakages to bring data from around the web into R on your local machine - so we mostly don’t do any dev for the web. However, the United States Geological Survey (USGS) recenty held an app competition - it was a good opportunity to play with R on the web. We won best overall app as described in an earlier post on this blog.

Revisiting our USGS app

rOpenSci’s activities and spaces are supported by a Code of Conductthat applies to all people participating in the rOpenSci community,including rOpenSci staff and leadership.It applies to all modes of interaction including GitHub project repositories,the rOpenSci discussion forum, Slack, Community Calls, Co-working and social sessions,and in person at rOpenSci-hosted events, including affiliated social gatherings.Our Code of Conduct is developed

rOpenSci Code of Conduct Annual Review

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

Openscapes

🔗Context setting  rOpenSci organizes monthly co-working hours on a variety of topics.But the constant is the quality of the discussion that ensues and the renewed energy that comes from it. The November coworking session welcomed Stefanie Butland from Openscapes as a co-host.She shared Openscapes’ approach of “Forking as a worldview”.Forks in the open-source software world refer to copies of an existing open-source project that add their own

The Dynamic Relationship of Forks with their Upstream Repository

This week we had a wonderful community call, From Novice to Contributor: Making and Supporting First-Time Contributions to FOSS, where Sunny Tseng, Pascal Burkhard, and Yaoxiang Li shared with us their experiences with, and advice for, first time contributors, with the excellent moderation of Hugo Gruson.This was a perfect start to our special series of activities to support first time contributors to Open Source Software.

Coworking Mini-Hackathon for First-Time 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  🔗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

Thanksgiving is celebrated in many parts of the world.The USA, rOpenSci’s official location, celebrates Thanksgiving this Thursday, 28th November.Giving thanks to contributors is also an important part of open-source software development.Many open-source software projects use the allcontributors.org system to acknowledge contributions, which includes One strong motivation for allcontributors.org is to “Recognize all contributors, including those

Give Thanks with the allcontributors Package

Since 2022, rOpenSci has been developing tools and processes to localize and translate our content.As a result of this effort, we created a set of guidelines to assist our community in translating and localizing our resources.What started as an internal challenge has evolved into a collaborative blueprint that we believe can help transform how scientific resources are shared in a multilingual research landscape.

Introducing the rOpenSci Localization and Translation Guidelines

We are excited to welcome Beatriz Milz and Margaret Siple to our team of Associate Editors for rOpenSci Software Peer Review.They join Laura DeCicco, Julia Gustavsen, Anna Krystalli, Mauro Lepore, Noam Ross, Maëlle Salmon, Emily Riederer, Adam Sparks, and Jeff Hollister.rOpenSci has been running a rigorous and collegial software peer review system since 2015.Editors manage the review process, performing initial package checks, identifying

Announcing New Software Peer Review Editors: Beatriz Milz and Margaret Siple

Our first cohort of the rOpenSci Champions Program has now completed the second phase of the program by developing their project and carrying out outreach activities. In this article, we share each Champion’s project, their achievements and their outreach activities. 🔗Champions’ Projects  In their applications Champions choose to develop a new package or to participate in the review process as authors or reviewers.

rOpenSci Champions Pilot Year: Projects Wrap-Up

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: Navigating the R ecosystem using R-Universe! On Tuesday, 24 September 2024 16:00 UTC (no RSVP needed), join us to learn more about R-Universe and how you can use it to improve your R package development workflow.

rOpenSci News Digest, August 2024

Now that you have created your package, presenting it to the world is a crucial step to

 gain visibility and attract users

. Marketing your package effectively contributes to reaching the people your package can support, finding users to assist you in maintaining and improving your package and allowing you to learn about how people use it. In this blog post we suggest a series of activities and tools for advertising your package.

Marketing Ideas For Your 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  🔗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

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.

rOpenSci News Digest, November 2023

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

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

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

We first introduced our Coworking andOffice Hour sessions in August 2021 after a successful pilot of several’label-athon’s in the April and May prior. We’ve had a successful couple of years since then and the coworking sessionshave evolved into themed events with different community hosts and me asa facilitator. It’s been a lovely change and we thought it was time to share these updates with the rOpenSci community! 🎉 🔗What are these sessions?

All About Coworking Sessions with rOpenSci

rOpenSci Champions Program Teams: Meet Victor Ordu and Laura DeCicco

I’m thrilled to share that CRediTas has passed peer review and been accepted to rOpenSci as well as to CRAN. I am glad to acknowledge the editor Emily Riedered and the two reviewers Marcelo S. Perlin and João Martins. Their comments and support were really insightful. CRediTas is a tiny package to facilitate the tedious job of creating CRediT authors statements for scientific publications.

CRediTas is Now Part of rOpenSci

🔗curl 5.0.0 is on CRAN  A new major version of the curl package has been released to CRAN. This release both brings internal improvements as well as new user-facing functionality, in particular with respect to concurrent downloads. From the NEWS file:curl 5.0.0 - New function multi_download() which supports concurrent downloads and resuming   download for large files, while giving detailed progress information.

curl 5.0.0: massive concurrent downloads and HTTP/2

🔗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

🔗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

🔗Why we created Computo  The idea of Computo was born out of a desire to foster a deeper scientific understanding as well as a need to address several challenges in the current scientific publishing landscape, especially within statistics and machine learning.

Computo - A Journal for Transparent and Reproducible Research in Statistics and Machine Learning

A bit more than one year ago, rOpenSci launched its new website design, by the designer Maru Lango. Not only did the website appearance change (for the better!), but the underlying framework too. ropensci.org is powered by Hugo, like blogdown!

An even better rOpenSci website with Hugo

Image processing is one of the core focus areas of rOpenSci. Over the last few months we have released several major upgrades to core packages in our imaging suite, including magick, tesseract, and av. This post highlights a few cool new features.

Updates to the rOpenSci image suite: magick, tesseract, and av

If you read my reflection #1 on rOpenSci Onboarding, then you know I see value in the Onboarding process. A LOT of value even. This post is about where that value lies. This question has important corollaries which I will explore here based on my experience as a reviewer of bowerbird:How is a package peer reviewer’s time best spent?When is the best time in a software package’s life cycle to undertake peer review?

Where is the value in package peer review?

rOpenSci

In my training as a AAAS Community Engagement Fellow, I hear repeatedly about the value of extending a personal welcome to your community members. This seems intuitive, but recently I put this to the test. Let me tell you about my experience creating and maintaining a #welcome channel in a community Slack group.

The Value of #Welcome

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

Twitter is one of the preferred social media platforms and networks for the R community and for the data, open science and research communities. Since the beginning of rOpenSci we have used Twitter to connect with our community and other parallel communities, to share what we do, and to be part of conversations around the topics important to our mission.

rOpenSci's Communication Channels: Twitter

I teach R to a lot of scientists, those that are new to science (i.e. students)as well as more established scientists, new to R.I find that after all their struggles of dealing with dates,or remembering where to put the comma, they’re so grateful to actual have an analysis,that they often forget or aren’t aware of the next steps.

How to Cite R and R Packages

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, July 2023

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

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

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, June 2024

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

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

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

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

This blog post is intended to help you get started in rOpenSci community by highlighting some key links and activities. If you have questions, please get in touch with our Community Manager, Yanina Bellini Saibene by email or schedule a meeting. We are here for you as you begin your journey with our community. Welcome! 🔗Where do I get started? Glad you asked!

How to Participate with rOpenSci

As a scientist who models plant diseases, I use a lot of weather data. Often this data is not available for areas of interest. Previously, I worked with the International Rice Research Institute (IRRI) and often the countries I was working with did not have weather data available or I was working on a large area covering several countries and needed a single source of data to work from.

Everybody talks about the weather

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

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

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

🔗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

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

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

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

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

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

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?

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.

The Fun of Building Things and the Challenge of Learning - the rOpenSci OzUnconf 2019

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?

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

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

New rOpenSci Packages for Text Processing in R

Our Community Call on December 15th covered a big topic in tech communities: “How do I create a code of conduct for my event/lab/codebase?”. Here, we cover some of the key themes and considerations that arose from the discussion and point to curated resources and examples to follow when developing a code of conduct (CoC) for your community. Three guest speakers shared different perspectives.

Highlights and Resources from Community Call v12: How do I create a code of conduct for my event/lab/codebase?

rOpenSci News Digest, February 2024

The iNaturalist project is a really cool way to both engage people in citizen science and collect species occurrence data. The premise is pretty simple, users download an app for their smartphone, and then can easily geo reference any specimen they see, uploading it to the iNaturalist website. It let’s users turn casual observations into meaningful crowdsourced species occurrence data.

Accessing iNaturalist data

A new package crul ison CRAN. crul is another HTTP client for R, but is relatively simplifiedcompared to httr, and is being builtto link closely with webmockr and vcr. webmockr andvcr are packages ported from Ruby’s webmockand vcr, respectively.They both make mocking HTTP requests really easy. A major use case for mocking HTTP requests is for unit tests.

crul - an HTTP client

Data on more than 10,000 species of ants recorded worldwide are available through from California Academy of Sciences’ AntWeb, a repository that boasts a wealth of natural history data, digital images, and specimen records on ant species from a large community of museum curators.

AntWeb - programmatic interface to ant biodiversity data

Natural history museums have long been valuable repositories of data on species diversity. These data have been critical for fostering and shaping the development of fields such as biogeography and systematics.

Introducing the ecoengine package

We are pleased to announce the release of our new Code of Conduct. rOpenSci’s community is our best asset and it’s important that we put strong mechanisms in place before we have to act on a report. As before, our Code applies equally to members of the rOpenSci team and to anyone from the community at large participating in in-person or online activities.

rOpenSci's new Code of Conduct

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.

The av Package: Production Quality Video in R

A few months ago, I wasn’t sure what to expect when looking at fluorescence microscopy images in published papers. I looked at the accompanying graph to understand the data or the point the authors were trying to make. Often, the graph represents one or more measures of the so-called co-localization, but I couldn’t figure out how to interpret them. It turned out; reading the images is simple.

Co-localization analysis of fluorescence microscopy images

At rOpenSci’s virtual HQ we’re busy planning out several exciting projects for the coming year thanks to the generous 180k grant from Sloan. In the interest of maintaining transparency with our community here are additional details of what we hope to accomplish and how we’ll measure our successes. We have also posted a full copy of our proposal over at figshare.

What we hope to accomplish with the new funding

citecorp is a new (hit CRAN in late August) R package for working with data from theOpenCitations Corpus (OCC).OpenCitations, run by David Shotton and Silvio Peroni,houses the OCC, an open repository of scholarly citation dataunder the very open CC0 license.

citecorp: working with open citations

Proper identification of individuals is crucial for acknowledging andstudying their scientific work, be it journal articles or pieces ofsoftware. In this tech note, one year after CRAN started supportingORCIDs, we shall explain why and how to use unique author identifiers inDESCRIPTION files. 🔗Why use ORCIDs on CRAN? When analyzing the authorship of CRAN packages, one can look at authors’names and email addresses.

Distinguish yourself in CRAN person() with ORCID

I’m happy to announce that I’ve started a project with rOpenSciunder their recent award from the Helmsley Foundation. My work with rOpenSci will focus on sustainability of the project itself. Sustainability can be defined as having theresources to do the necessary work to continue and grow rOpenSci. This is one of the most difficult challenges forrOpenSci and for many other research software projects.

Software sustainability research with rOpenSci

We have started a new R package interacting with NOAA climate data called

 rnoaa

. You can find our package in development here and documentation for NOAA web services here. It is still early days for this package, but we wanted to demo what you can do with the package.

NOAA climate sparklines

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

Chat with the rOpenSci team at upcoming meetings

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

The rOpenSci Unconference is coming to Australia and we are excited!!  The event will take place in sunny Brisbane, on April 21-22 2016 hosted at the Microsoft Innovation Centre.

Australian rOpenSci Unconference

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

We have previously written about creating interactive maps on the web from R, with the interactive maps on Github. See here, here, here, and here. A different approach is to use CartoDB, a freemium service with sql interface to your data tables that provides a map to visualize data in those tables.

Species occurrence data to CartoDB

A new R package, cffr, has beendeveloped,peer-reviewed byrOpenSci and accepted by CRAN. Thispackage has a single purpose: to create a valid CITATION.cff file using themetadata of any R package. 🔗CITATION.cff files and why they matter A Citation File Format (CFF) is aplain text file with human- and machine-readable citation information forsoftware (and datasets)

 1

. Under the hood, a CFF file is a YAML file.

cffr: Create a CITATION.cff File for your R Package

🔗What is Taxonomy? Taxonomy in its most general sense is the practice and science of classification. It can refer to many things. You may have heard or used the word

 taxonomy

used to indicate any sort of classification of things, whether it be companies or widgets. Here, we’re talking about biological taxonomy, the science of defining and naming groups of biological organisms.

The rOpenSci Taxonomy Suite

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

🔗Hello! I am Yanina Bellini Saibene, your new community manager. I’m so excited to join rOpenSci in this role, and support such an important project in open science and in the R Community.

Introducing rOpenSci new Community Manager, Yanina Bellini Saibene

🔗TL;DR  rsnps is a package that enables the retrieval of single nucleotide polymorphism (SNP) data from the  NCBI’s dbSNP database and openSNP by providing wrappers for the APIs. Single nucleotide polymorphisms represent differences at one specific position in a detected biological sequence compared to the reference. ncbi_snp_query() now returns all reported variant allele frequencies in dbSNP in column maf_population in form of a tibble.

rOpenSci - open tools for open science