Open Tools and R Packages for Open Science

Jeroen Ooms

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

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 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

Maëlle Salmon

Zhian N. Kamvar

Zhiam Kamvar is Lesson Infrastructure Technology Developer at The Carpentries (Software Carpentry, Data Carpentry &amp; Library Carpentry), an open global community teaching the skills &amp;

Communication &amp; Collaboration with Contributors in an Open-Source Organization

Kari Norman

Dealing with taxonomic inconsistencies within and across datasets is a fundamental challenge of ecology and evolutionary biology. Accounting for species synonyms, taxa splitting and unification is especially important as aggregation of data across time and different data sources becomes increasingly common.

taxadb: A High-Performance Local Taxonomic Database Interface

Scott Chamberlain

We just released a new version of taxize - version 0.2.0. This release contains a number of new features, and bug fixes. Here is a run down of some of the changes: First, install and load taxize  install.packages("rgbif") library(taxize) New things  New functions: class2tree   Sometimes you just want to have a visual of the taxonomic relationships among taxa.

New features in the most recent taxize update, v0.2

Jessie Roberts

Miles McBain

Nicholas Tierney

On April 21st and 22nd of 2016, we had 40 members of the R community gather in Brisbane, Australia, with the goal of reproducing the rOpensci Unconference events that have been running with great success in San Francisco since 2014. Like every event organisers ever, we went through the usual crisis: Where will it be? Will anyone actually show up? Is the problem space over venue, date, attendees, catering, sponsors convex?

Australia Unconference

Open access week is here! We love open access, and think it’s extremely important to publish in open access journals. One of the many benefits of open access literature is that we likely can use the text of articles in OA journals for many things, including text-mining. What’s even more awesome is some OA publishers provide API (application programming interface) access to their full text articles.

OA week - A simple use case for programmatic access to PLOS full text

Yanina Bellini Saibene

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

The USGS recently released a way to search for and get species occurrence records for the USA. The service is called BISON (Biodiversity Information Serving Our Nation). The service has a web interface for human interaction in a browser, and two APIs (application programming interface) to allow machines to interact with their database.

BISON USGS species occurrence data

rOpenSci

Stefanie Butland

The title of this post refers to Hacktoberfest, a month-long event organized annually by Digital Ocean to encourage contributions to open source projects on GitHub.Unfortunately, this October, many maintainers are dealing with spam pull requests.So instead of issuing a general appeal to participate, we’re pointing you to our new Community Contributing Guide’s section dedicated to our open Issues List.Along with showing you how to find help

Hacktober? Any Month is a Good Month to Contribute to rOpenSci

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

Karthik Ram

Today we are pleased to announce that rOpenSci has been awarded a generous 180K grant from the Alfred P. Sloan foundation. This funding will allow us to develop a whole new suite of tools and provide scientists with general purpose toolkits to access various kinds of scientific data. We will also be traveling a whole bunch this year and running workshops at several conferences and universities.

rOpenSci awarded 180K from The Sloan Foundation

Ignasi Bartomeus

The following was a guest post from Ignasi Bartomeus, originally posted on his blog on 26 Nov, 2012. Check out a related blog post here. Note the functionality discussed in this post is now in our taxize package under the function gisd_isinvasive. We hacked out a quick Shiny app so you can play around with the below function in taxize on the web to get invasive status and plot it on a phylogeny. Check it out here.

is.invasive()

We have been writing code for R packages for a couple years, so it is time to take a look back at the data. What data you ask? The commits data from GitHub ~ data that records who did what and when. Using the Github commits API we can gather data on who commited code to a Github repository, and when they did it. Then we can visualize this hitorical record.

Visualizing rOpenSci collaboration

Mark Padgham

Kara Woo

We are pleased to announce the release of

 Version 2.4

of our Code of Conduct with changes based on the feedback of our community. What’s new? Greater detail about acceptable and unacceptable behaviors in online settings. First translation of the text to Spanish. You can access now the last version full-text in English and Spanish. We welcome your feedback by email to conduct at ropensci.org.

rOpenSci Code of Conduct Update

Steffi LaZerte

Maintaining a package can be a lonesome activity, which sometimes poses a problem if you prefer team work or if you encounter a very thorny-for-you problem.Beside belonging to a supportive community of maintainers (like rOpenSci 😉), for collaborative help and commiseration you can try to build a community of contributors around your package!In this post, we’ll explore one tool helping you towards that goal: “help wanted” issues, with which your

Attract Contributors with 'help wanted' Issues

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

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

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

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

Can you think of an rOpenSci community member that you’d like to thank?A reviewer who helped you improve your package?Someone who answered your question?A community call speaker from whom you gained insight?Someone who encouraged you behind the scenes?

Thank You to the rOpenSci Community, 2021

Dear rOpenSci friends, it’s time for our monthly news roundup!

rOpenSci News Digest, July 2021

Noam Ross

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

In a recent blog post we discussed caching calls to the web offline, on your own computer. Just like you can cache data on your own computer, a data provider can do the same thing. Most of the data providers we work with do not provide caching. However, at least one does: EOL, or Encyclopedia of Life.

Caching Encyclopedia of Life API calls

Carl Boettiger

We’re happy to announce the launch of a CRAN-style repository for rOpenSci at http://packages.ropensci.org  This repository contains the latest nightly builds from the master branch of all rOpenSci packages currently on GitHub.

A drat repository for rOpenSci

In a year where it has been hard to pay attention to anything not critical to our day-to-day lives, you have continued to share your time, expertise, enthusiasm, and willingness to try things with us. Our staff of developers, researchers, and community builders work to create technical and social infrastructure to lower barriers to working with research data, and you, our community, continually help us push farther.

Thank You to the rOpenSci Community, 2020

Laura DeCicco

Julia Gustavsen

Jeff Hollister

Anna Krystalli

Mauro Lepore

Emily Riederer

Adam Sparks

Melina Vidoni

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 0.8.0, with all changes listed in the changelog.Farewell Stefanie Butland  After many years of fabulous contributions to the rOpenSci community, Stefanie Butland left the role of community manager at the start of 2022.

rOpenSci Dev Guide 0.8.0: Updates

Dear rOpenSci friends, it’s time for our monthly news roundup!Some housekeeping first:We’ve been changing the infrastructure of our newsletter a bit so please update your RSS and JSON feeds to https://ropensci.org/tags/newsletter/index.xml and https://ropensci.org/tags/newsletter/index.json, respectively.You can read this post on our blog.Now let’s dive into the activity at and around rOpenSci!rOpenSci HQ  Our R-universe project now has its own

Latest rOpenSci News Digest

Carson Sievert

Editor’s note: This is the first in a series of posts from rOpenSci’s recent hackathon.

I recently had the pleasure of participating in rOpenSci’s hackathon. To be honest, I was quite nervous to work among such notables, but I immediately felt welcome thanks to a warm and personable group. Alyssa Frazee has a great post summarizing the event, so check that out if you haven’t already.

Topic modeling in R

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

Ted Hart

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

Alejandra Bellini

Lucio Casalla

Rich FitzJohn

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: The R-Universe Against Diseases.

Just a quick note that the Task View we have been working on with others

 Web Technologies and Services

is up on CRAN now. Find it here https://cran.r-project.org/web/views/WebTechnologies.html. This is the first version - there are definitely changes to come. Changes are being suggested as I write this on Twitter… The draft version of the task view is on Github here if you want to file an issue.

Web Technologies and Services taskview is up on CRAN

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

One of our primary goals at ROpenSci is to wrap as many science API’s as possible. While each package can be used as a standalone interface, there’s lots of ways our packages can overlap and complement each other. Sure He-Man usually rode Battle Cat, but there’s no reason he couldn’t ride a my little pony sometimes too. That’s the case with our packages for GBIF and the worldbank climate data api.

Overlaying climate data with species occurrence data

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

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  A first package was submitted to rOpenSci Statistical Software Peer Review, two months after its opening: the tsbox package by Christoph Sax.We are very excited, and thankful for the opportunity to hone our new software review tooling!

rOpenSci News Digest, September 2021

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

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

rOpenSci Software Peer Review and Statistical Software Peer Review rely on the volunteer work of reviewers, and editors.Editors manage the day-to-day flow of submissions, recruit reviewers and guide the peer-review process from start to finish.

Editorial Challenges and Solutions in Software Peer Review

Athanasia Mo Mowinckel

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

Rob Kooper

Chris Black

Eric Scott

Michael Dietze

David LeBauer

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

Real use cases from people using our software are awesome. They are important for many reasons: 1) They make the code more useable because we may change code to make the interace and output easier to understand; 2) They may highlight bugs in our code;

Use case - how to get species occurrence data from GBIF for a genus

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

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

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’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

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

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

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

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

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

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

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

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

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

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

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

Os Keyes

There are two things that make R such a wonderful programming environment - the vast number of packages to access, process and interpretdata, and the enthusiastic individuals and subcommunities (of which rOpenSci is a great example). One, of course, flows from the other:R programmers write R packages to provide language users with more features, which makes everyone’s jobs easier and (hopefully!)attracts more users and more contributions.

Introducing a Wishlist for Scientific R Packages

We have a number of packages for getting species occurrence data: rgbif and rbison. The power of R is that you can pull down this occurrence data, manipulate the data, do some analyses, and visualize the data - all in one open source framework. However, when dealing with occurrence data on maps, it is often useful to be able to interact with the visualization.

From occurrence data to interactive maps on the web

We have released updates for the rOpenSci text analysis tools. This technote will highlight some of the major improvements in the spelling package and also the underlying hunspell package, which provides the spelling engine for the spelling package. install.packages("spelling")  Update to the latest versions to use these cool new features!

Spelling 2.0: Improved Markdown and RStudio Support

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

Rafael Pilliard Hellwig

Background   Surveys are ubiquitous in the social sciences, and the best of them are meticulously planned out. Statisticians often decide on a sample size based on a theoretical design, and then proceed to inflate this number to account for “sample losses”. This ensures that the desired sample size is achieved, even in the presence of non-response.

outcomerate: Transparent Communication of Quality in Social Surveys

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?

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 - open tools for open science

phylotaR: Retrieve Orthologous Sequences from GenBank