rOpenSci - open tools for open science

Blog post, GitHub repository

What did you do?

I used targets to analyze and report on omics (metabolomics in this case) data analysis.

URL or code snippet for your use case*

Image

Sector

academic

Field(s) of application

biomedical research

Social Handles

Mastodon: https://mastodon.social/@rmflight

rOpenSci Champions Program Teams: Meet Ghozayel Elotteebi and Zebulun Arendsee

Fri, 23 Jun 2023 00:00:00 +0000

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. In our program, each Champion has a mentor who accompanies them during their training and development of their project.

In this series of blog posts, we introduce you to the ten teams of this first cohort and what they will be working on in the program.

rOpenSci News Digest, June 2023

Thu, 22 Jun 2023 00:00:00 +0000

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. To share some of these community stories, we created the rOpenSci interview series “Meeting the stars of the R-Universe”.

All About Coworking Sessions with rOpenSci

Wed, 21 Jun 2023 00:00:00 +0000

We first introduced our Coworking and Office 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 sessions have evolved into themed events with different community hosts and me as a facilitator. It’s been a lovely change and we thought it was time to share these updates with the rOpenSci community! 🎉

rOpenSci Champions Program Teams: Meet Alican Cagri Gokcek and Elio Campitelli

Mon, 19 Jun 2023 00:00:00 +0000

In this series of blog posts, we introduce you to the ten teams of this first cohort and what they will be working on in the program.

How do you measure the impact of a champions program?

Thu, 15 Jun 2023 00:00:00 +0000

This post can also be found on the CSCCE blog."

How do you measure the impact of a champions program? This was the central question of a working session at CZI’s Accelerating Open Science in Latin America workshop, convened by rOpenSci’s Community Manager Yani Bellini Saibene and attended by CSCCE’s Founder and Director, Lou Woodley.

Measuring the impact of any kind of community program presents a series of challenges:

What is the impact that you’re hoping your program will have?

rOpenSciの紹介

Wed, 14 Jun 2023 09:00:00 +0000

rOpenSci's Communication Channels for Safe and Friendly Exchange

Wed, 14 Jun 2023 00:00:00 +0000

Read it in: Español.

As we anticipated in November 2022 the changes implemented by Twitter have generated a less safe and friendly space for our community. That is why from June 2023, we will stop interacting on this platform. We will maintain the account in hopes that we can return when Twitter is once again a safe and supportive space, but in the meanwhile will focus our communication efforts elsewhere.

We understand that until now Twitter has been one of the reference platforms for the R community, data, research and open science community but we have to be responsible and coherent with the spaces we choose for exchange and interaction and our values as a community and organization.

rOpenSci Champions Program Teams: Meet Cheryl Isabella Lim and Mauro Lepore

Mon, 12 Jun 2023 00:00:00 +0000

In this series of blog posts, we introduce you to the ten teams of this first cohort and what they will be working on in the program.

Social Coworking and Office Hours - Integrating and merging datasets from different sources

Tue, 06 Jun 2023 03:00:00 +0000

Join us for 2 hours Tuesday June 06, 09:00 Australian Western (01:00 UTC) for Social Coworking + Office Hours

This month we’re focusing on the theme Integrating and merging datasets from different sources with community host Cynthia Huang who has been tackling how to integrate data from multiple sources as part of her PhD at Monash University!

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

Tue, 06 Jun 2023 00:00:00 +0000

Read it in: Español.

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. Be sure to watch the video at the end with excerpts from the interview.

Troubleshooting Pandoc Problems as an R User

Thu, 01 Jun 2023 00:00:00 +0000

Read it in: Français.

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 anecdotally useful: it’s part of the R Markdown machinery, and powers Quarto. So, whether you’re juggling documents in various formats or simply trying to publish your reproducible analysis, you might have been using Pandoc (even if you didn’t know!), or maybe you should be using Pandoc.

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

Wed, 31 May 2023 00:00:00 +0000

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. By default it returns a zip file with all the packages, binaries, and documentation in your repository. If this is more than you need, there are parameters to include e.g. only binaries for certain platforms or certain versions of R, or to create a repository from a subset of the packages in your universe. Explore the parameters on the API tab of any universe, for example: https://ggseg.r-universe.dev/api

Developing Software Together (training for champions program applicants)

Fri, 19 May 2023 17:00:00 +0000

rOpenSci News Digest, May 2023

Fri, 19 May 2023 00:00:00 +0000

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

Statistical software review updates

We are very happy to welcome Jouni Helske to the editorial team for statistical software review. Jouni jumped straight in to act as editor for the fwildclusterboot submission, an exciting first extension of our system beyond R alone to include functions in the Julia language. We have so far approved eight packages, five of which have a silver badge, and three gold, with two further packages currently under review.

How to contribute to base R (champions training)

Thu, 18 May 2023 17:00:00 +0000

rOpenSci Champions Program Teams: Meet César and Marc

Thu, 18 May 2023 00:00:00 +0000

In this series of blog posts, we introduce you to the ten teams of this first cohort and what they will be working on in the program.

Scheduling Mastodon Posts in R with rtoot and GitHub Actions

Wed, 17 May 2023 00:00:00 +0000

A lot of what I do as rOpenSci’s community assistant is related to social media. I check for posts about rOpenSci packages, invite people to share usecases, advertise upcoming events, as well as promoting new packages which completed software peer review.

Up until this past year most of this work was focused on Twitter and because we want to reach an international audience, we used Tweetdeck to schedule posts for different timezones¹. Being able to see when posts were queued was also important for us as a team to better plan our post timing.

CRediTas is Now Part of rOpenSci

Tue, 16 May 2023 00:00:00 +0000

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. Normally, the first author of a scientific paper organizes a table in a spreadsheet where all the authors self-state their contributions. Often too, it is the first author’s responsibility to state the contributions of all co-authors. However, at the end, the information has to be translated to the CRediT statement format of “Author 1: roles Authors 2: roles …” which is prone to errors and tedious, especially if there are many co-authors. The CRediTas package aims to make this easier by providing a template to be filled in form of a table (csv) and then converting this table to CRediT statement format.

rOpenSci Champions Program Teams: Meet Victor Ordu and Laura DeCicco

Thu, 11 May 2023 00:00:00 +0000

In this series of blog posts, we introduce you to the ten teams of this first cohort and what they will be working on in the program.

Programming for Science

Wed, 10 May 2023 11:00:00 +0000

rOpenSci Champions Program Teams: Meet Haydée Svab and Beatriz Milz

Tue, 09 May 2023 00:00:00 +0000

In this series of blog posts, we introduce you to the ten teams of this first cohort and what they will be working on in the program.

Preparing remote sensing data for deep learning using r-spatial

Mon, 08 May 2023 09:00:00 +0000

rOpenSci Champions Program Teams: Meet Carolina Pradier and Athanasia Monika Mowinckel

Fri, 05 May 2023 00:00:00 +0000

In this series of blog posts, we introduce you to the ten teams of this first cohort and what they will be working on in the program.

Social Coworking and Office Hours - Spring Cleaning for R packages and Scripts

Tue, 02 May 2023 18:00:00 +0000

Join us for 2 hours Tuesday May 02, 09:00 Americas Pacific (16:00 UTC) for Social Coworking + Office Hours

This month we’re focusing on the theme Spring Cleaning* with Steffi LaZerte, rOpenSci’s community assistant who forgets all too often to spring clean her own packages 😱.

* For those of us in the Northern Hemisphere and Fall Cleaning for our Southern friends.

rOpenSci Champions Program Teams: Meet Bilikisu Wunmi Olatunji and Christina Maimone

Tue, 25 Apr 2023 00:00:00 +0000

In this series of blog posts, we introduce you to the ten teams of this first cohort and what they will be working on in the program.

rOpenSci News Digest, April 2023

Fri, 21 Apr 2023 00:00:00 +0000

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

Tell me who you hang out with and I will tell you who you are. A collaborations analysis using social networks analysis

Thu, 20 Apr 2023 17:35:00 +0000

How to enable and sustain thriving Open Source Ecosystems (OSE).

Wed, 19 Apr 2023 17:00:00 +0000

rOpenSci Champions Program Teams: Meet Marcos Prunello and Lukas Wallrich

Tue, 18 Apr 2023 00:00:00 +0000

In this series of blog posts, we introduce you to the ten teams of this first cohort and what they will be working on in the program.

rOpenSci Champions Program Teams: Meet Pao Corrales and Adam Sparks

Thu, 13 Apr 2023 00:00:00 +0000

In this series of blog posts, we introduce you to the ten teams of this first cohort and what they will be working on in the program.

How rOpenSci performs peer-review (champions training)

Tue, 04 Apr 2023 17:00:00 +0000

Social Coworking and Office Hours - Working with taxonomic lists in R

Tue, 04 Apr 2023 14:00:00 +0000

Join us for 2 hours Tuesday April 04, 14:00 European Central (12:00 UTC) for Social Coworking + Office Hours

This month we’re focusing on the theme Working with taxonomic lists in R with community host Miguel Alvarez, maintainer of the rOpenSci package taxlist.

Come for the full 2 hrs or only as long as you need!

waywiser is Now a Part of rOpenSci

Tue, 04 Apr 2023 00:00:00 +0000

I’m thrilled to share that waywiser, my R package focused on providing framework-agnostic (but tidymodels-friendly) methods for assessing models fit to spatial data¹, has passed peer review and been accepted to rOpenSci. As always, the review process improved the package immensely, thanks to the thoughtful reviews of Virgilio Gómez-Rubio and Jakub Nowosad², as well as the shepherding of Anna Krystalli and Paula Moraga as editors.

As of Monday, March 20th, the reviewed version has officially made its way to CRAN. This is a huge update, bringing in a ton of new functions and improving consistency and speed across the package, and I’m excited to have it officially released.

How r-universe searches for packages on CRAN / Bioconductor

Mon, 03 Apr 2023 00:00:00 +0000

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. These are a mix of packages found on popular networks like CRAN or Bioconductor, and packages that were registered by users.

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

Thu, 30 Mar 2023 00:00:00 +0000

Read it in: Español.

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 Norway to talk with Athanasia Monika Mowinckel. Be sure to watch the video at the end with excerpts from the interview.

Package Development: Not Rocket Science (champions training)

Thu, 23 Mar 2023 11:00:00 +0000

rOpenSci News Digest, March 2023

Fri, 17 Mar 2023 00:00:00 +0000

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

Package Development: the Mechanics (champions training)

Tue, 14 Mar 2023 14:00:00 +0000

Social Coworking and Office Hours - Checking data with naniar, visdat, assertr, and skimr

Tue, 07 Mar 2023 03:00:00 +0000

Join us for 2 hours Tuesday March 07, 09:00 Australian Western (01:00 UTC) for Social Coworking + Office Hours

This month we’re focusing on the theme Checking data with naniar, visdat, assertr, and skimr with community host Nick Tierney, R enthusiast and author of several R packages (including naniar and visdat!).

Come for the full 2 hrs or only as long as you need!

Meeting the Stars of the R-universe: ThinkR's Approach to Contributing to a Growing and Friendly R Community

Tue, 28 Feb 2023 00:00:00 +0000

Read it in: Español.Read it in: Français.

This is the second 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.

We continue our journey in France with Sébastien Rochette, R Expert at ThinkR, a company focused on teaching and training as well as developing open source R packages. Be sure to watch the video at the end with excerpts from the interview.

Sébastien Rochette
Head of Production at ThinkR

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

Mon, 27 Feb 2023 00:00:00 +0000

Read it in: Español.

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.

rOpenSci. Reproducible Open Science for (and by) All

Thu, 23 Feb 2023 13:15:00 +0000

rOpenSci Champions Program. Mentorship Training and Orientation

Tue, 21 Feb 2023 14:00:00 +0000

rOpenSci Champions Program Kick off

Tue, 21 Feb 2023 00:00:01 -0600

Read it in: Español.

The Champions Program got off to a great start in 2023!

We’re happy to report on the first couple of months in our first run of the rOpenSci Champions Program. In September 2022, we launched the program, advertising for both mentors and mentees to apply.

We received a total of 102 applications from 31 different countries. Seventy-four applications were for champions and twenty eight for mentors. We are very grateful to everyone who took the time to apply to our program.

rOpenSci News Digest, February 2023

Fri, 17 Feb 2023 00:00:00 +0000

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!

We have changed the preferred git repo name where you host your packages.json registry for R-universe, see our post New preferred repo name for r-universe registries. We now recommend to use the full lowercase name of your R-universe domain as the repo name, for instance TileDB-Inc/tiledb-inc.r-universe.dev.

rOpenSci Champions Program. A mentoring & training program for Scientific Open Source Champions

Thu, 16 Feb 2023 11:00:00 +0000

Multilingual Publishing

Thu, 09 Feb 2023 09:00:00 +0000

Social Coworking and Office Hours - Setting up Continuous Integration

Tue, 07 Feb 2023 19:00:00 +0000

Join us for 2 hours Tuesday February 07, 09:00 Americas Pacific (17:00 UTC) for Social Coworking + Office Hours

This month we’re focusing on the theme Setting up Continuous Integration (CI) with community host Hugo Gruson, Research Software Engineer in Epidemiology and CI/automation addict.

Come for the full 2 hrs or only as long as you need!

New preferred repo name for r-universe registries

Tue, 07 Feb 2023 00:00:00 +0000

Running your own package registry

Tiny update for r-universe users whos run their own package registry: we have changed the preferred git repo name where you host your packages.json registry file.

Previously the git repository was simply called universe, i.e. the registry for tiledb-inc.r-universe.dev was in the GitHub repository tiledb-inc/universe. We now recommend to instead use the full lowercase name of your r-universe domain as the repo name, i.e tiledb-inc/tiledb-inc.r-universe.dev.

For now the old name universe will keep working as well, but this will be deprecated in 2024 so we recommend renaming it now.

What Does It Mean to Maintain a Package?

Tue, 07 Feb 2023 00:00:00 +0000

Read it in: Español.Read it in: Português.

Part of what we aim to do at rOpenSci is nurture a community of package maintainers who help each other. In addition to support during package maintenance, we also want to support maintainers who wish to move on. Situations can change, and there may come a time when a maintainer is looking to pass maintenance on to another. If a maintainer finds themself in this situation and would like to transfer maintainership, we help by advertising, and also help the new maintainer(s) with advice, generally à la “look around to see if anything needs fixing, then do routine maintenance”. But what is routine maintenance? This post is an attempt to define what package maintenance entails, with a few tips.

{targets} in Action

Fri, 06 Jan 2023 00:00:00 +0000

The {targets} package is a pipeline tool for Statistics and data science in R. With {targets}, you can maintain a reproducible workflow without repeating yourself. {targets} learns how your pipeline fits together, skips costly runtime for tasks that are already up to date, runs only the necessary computation, supports implicit parallel computing, abstracts files as R objects, and shows tangible evidence that the results match the underlying code and data.

On this call Will, Eric and Joel will share their experience putting {targets} into action. Eric will share with us Using {targets} with HPC and Joel will talk about Using {targets} for bioinformatics pipelines, then Will will demonstrate Debugging {targets} pipelines.

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

Tue, 31 Jan 2023 00:00:00 +0000

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 panel models called the Bayesian dynamic multivariate panel model (DMPM) which supports

Improved permanent URL schema for r-universe.dev

Mon, 30 Jan 2023 00:00:00 +0000

Pretty permanent URLs!

We have improved the URL schema for the r-universe.dev front-end to make it even easier to find and share a link to an R package, article, API, or other resource.

The old URLs will now automatically be redirected to the new locations, so this should be a non-breaking change. But of course we recommend updating your references to link to the new permanent URLs.

rOpenSci News Digest, January 2023

Fri, 20 Jan 2023 00:00:00 +0000

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

{targets} in Action Community Call

Tuesday, 31 January 2023 20:00 UTC / Tuesday, 31 January 2023 15:00 EST / Wednesday, 1st February 07:00 AEDT.

curl 5.0.0: massive concurrent downloads and HTTP/2

Fri, 13 Jan 2023 00:00:00 +0000

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.
- Windows: updated libcurl to 7.84.0 + nghttp2
- Windows: default to CURLSSLOPT_NATIVE_CA when using openssl unless an ennvar
with CURL_CA_BUNDLE is set.
- Use the new optiontype API for type checking if available (libcurl 7.73.0)

The curl package is used by most other R packages for performing HTTP requests. Over 60% of rOpenSci packages directly or indirectly depend on curl for network interaction, hence improvements and bugs in curl have a big impact on the entire ecosystem.

Expanding our Community through Multilingual Publishing

Thu, 12 Jan 2023 00:00:00 +0000

Read it in: Español.

We are excited to announce that, with the support of the Chan Zuckerberg Initiative, NumFOCUS, and the R Consortium, we have begun the process of translating rOpenSci’s materials on best practices for software development, code review, and contribution to open source projects into Spanish. As part of this effort, we are also developing guidelines and tools for translating open source resources to reach a wider audience.

According to a recent report from The Linux Foundation, language access is one of the environmental barriers to equity in open source. The report states that

Social Coworking and Office Hours - Working with new R users

Tue, 10 Jan 2023 15:00:00 +0000

Join us for 2 hours Tuesday January 10, 14:00 European Central (13:00 UTC) for Social Coworking + Office Hours

This month we’re focusing on the theme Working with new R users with community host Alex Koiter, who is a professor in Geography and is enthusiastic about introducing R to undergraduate students.

Come for the full 2 hrs or only as long as you need!

rOpenSci 2022 Code of Conduct Transparency Report

Fri, 06 Jan 2023 00:00:00 +0000

rOpenSci Code of Conduct Annual Review

Fri, 06 Jan 2023 00:00:00 +0000

This report presents our annual review of the rOpenSci Code of Conduct, reporting process, and internal guidelines for handling reports and enforcement.

Updates

Changes to the text, including addition of greater detail about acceptable and unacceptable behaviors in online settings.
Added a new language, through doing the first translation of the text to Spanish.
Changes to the committee. We thank Megan Carter for serving as independent community member until June 2022 and welcome back Kara Woo to serve in this role. Yanina Bellini Saibene joins the committee as the new rOpenSci Community Manager.
Review of our processes. We reviewed our onboarding and offboarding process for the code of conduct committee and generated templates for incident management.

These changes were released July 7, 2022 as version 2.4.

rOpenSci News Digest, December 2022

Fri, 16 Dec 2022 00:00:00 +0000

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

You can read this post on our blog. Now let’s dive into the activity at and around rOpenSci!

rOpenSci HQ

One-page HTML package manuals on R-universe!

We have recently started building HTML reference manuals for each package in the R-universe! For packages that have had an update in the past 3 weeks, the reference manual is now linked from the package homepage on R-universe.dev. All packages in the R-universe are rebuilt at least once per month, so soon all packages should have an online HTML manual. You can also find reference manuals for base-R packages.

Social Coworking and Office Hours - Getting started with targets!

Tue, 06 Dec 2022 03:00:00 +0000

Join us for 2 hours Tuesday, December 6th, 9 AM Australian Western / 1:00 UTC for
Social Coworking + Office Hours

This October we’re focusing on the theme Getting started with targets! with community host Nick Tierney, R and targets enthusiast and author of several R packages.

Come for the full 2 hrs or only as long as you need!

How to Save ggplot2 Plots in a targets Workflow?

Tue, 06 Dec 2022 00:00:00 +0000

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.

I want to keep my plots accessible to be able to revisit them any time and to assemble them with patchwork into more complex figures for a potential paper. In a regular project I generate 10 to 20 figures, some only diagnostic ones and some polished ones for the finished manuscript. I do revisit the list of figures often, as co-authors or reviewers ask me for more detailed analyses and visualizations.

Our First Peer-Reviewed Statistical R Packages!

Wed, 30 Nov 2022 00:00:01 -0700

rOpenSci is very excited to announce our first peer-reviewed statistical R packages!

One of rOpenSci’s core programs is software peer-review, where we use best practices from software engineering and academic peer-review to improve scientific software. Through this, we aim to make scientific software more robust, usable, and trustworthy, and build a supportive community of practitioners.

Historically, we have focused on R packages that manage the research data life cycle. Now, thanks to work over the past two years supported by the Sloan Foundation we also facilitate peer-review of packages that implement statistical algorithms. The first statistical packages to pass peer review are:

postdoc 1.0: minimal and uncluttered HTML package manuals

Tue, 29 Nov 2022 00:00:00 +0000

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. Try it yourself:

# Download and install postdoc in R
install.packages('postdoc',
 repos = c('https://ropensci.r-universe.dev','https://cloud.r-project.org'))

# Generate a manual for 'jsonlite'
html <- postdoc::render_package_manual("jsonlite", ".")
utils::browseURL(html)

We have recently started building the reference manuals for each package r-universe: for packages that have had an update in the past 10 days, the reference manual is now linked from the package homepage on r-universe.dev. All packages in in r-universe gets rebuilt at least once per month, so soon all packages should have the manual. Postdoc reference manuals for base-R packages can be found here.

Meeting the stars of the R-universe: R Community, Exchange and Learn

Wed, 23 Nov 2022 00:00:00 +0000

Read it in: Español.

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. We begin our journey in Argentina with a team that uses R and develops R packages for the Argentinean State. Be sure to watch the video at the end with excerpts from the interview.

Delete all your tweets using rtweet

Tue, 22 Nov 2022 00:00:00 +0000

rOpenSci package or resource used

What did you do?

Worried about how a certain social media platform is going and want to start reducing your footprint there? If you are looking to remove yourself Twitter, you can entirely delete your account, but I’ve seen some folks say a better initial move may be to delete the content from your account (perhaps including followers and following), and then take your account private or deactivate it. This has the benefit of you keeping control of your username. In this blog post, I walked through how to use rtweet to automate some of these steps. I deleted about 25,000 tweets using this method!

rOpenSci News Digest, November 2022

Fri, 18 Nov 2022 00:00:00 +0000

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

Multilingual Publishing

Open Source and Open Science are global movements, but most of their material and resources are published in English, meaning non-English speakers face a significant barrier to being part of these movements.
Publishing multilingual resources can lower these barriers by increasing access to knowledge, which helps democratize access to quality resources, and therefore increases the potential for contributing to software and open science projects.

rOpenSci's Communication Channels: Twitter

Wed, 16 Nov 2022 00:00:00 +0000

Read it in: Español.

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.

We aim to provide a safe and friendly space for everyone in our community, and this influences how we choose which spaces we use to interact with our community members.

Adding missing EXIF data to wildlife trail camera images

Thu, 10 Nov 2022 00:00:00 +0000

rOpenSci package or resource used*

Editing metadata in trail camera images using R, magick and exiftool

What did you do?

Use R/magick in combination with ffmpeg and exiftool, to add geolocation and date-time metadata to images where metadata was not created by the camera.

URL or code snippet for your use case*

Image

Sector

Other

Field(s) of application

ecology, citizen science

rOpenSci. Bringing the best parts of academic peer-review to research software

Fri, 04 Nov 2022 20:00:00 +0000

The Challenges & Opportunities of Sustaining Open Source Ecosystems

Fri, 04 Nov 2022 18:00:00 +0000

Our Project Lead and co-founder Karthik Ram gave a talk on Open Source Ecosystems (OSEs) at the Open Innovation for Earth Observation Programmes workshop organized by ESA and NASA in Frascati.

In this talk, Karthik describe how The rOpenSci Project began as a small club (using Nadia Asparouhova’s terminology) and grew into a modest federation by engaging the community collaboration models described by CSCCE. We started out by conveying tools, then accepting contributions, collaborating with researchers via the peer-review system, and finally enabling co-creation via the r-universe. Karthik then cover how organizations like space agencies can stand up lightweight OSPOs to start, and use metrics (like those from CHAOSS) to help open-source projects thrive and succeed. Karthik then cover the various factors necessary to turn a nascent project into an OSE from early conversations as part of my newly funded POSE training program.

Social Coworking and Office Hours - Champions Program Application Clinic

Tue, 01 Nov 2022 18:00:00 +0000

Join us for 2 hours Tuesday, November 1st, 9 AM North American Pacific / 16:00 UTC for Social Coworking + Office Hours

This month we have a special session operating as an Application Clinic for the Champions Program with our community manager, Yanina Bellini Saibene, as co-host!

Come for the full 2 hrs or only as long as you need!

Mentoring & training program for Scientific Open Source Champions

Fri, 23 Sep 2022 00:00:00 +0000

On this call Santosh and Emanuele will share their experience of being champions in their communities. We will highlight the benefits of being part of a champions program for you and for your community, what kind of learning, activities and opportunities an open source community champions program provides. Yani will present the details of our Champion Program and answer all your question about it.

rOpenSci News Digest, October 2022

Fri, 21 Oct 2022 00:00:00 +0000

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 Champions Program: call for Champions and call for Mentors

The rOpenSci Champions Program is part of a series of activities and projects we are carrying out to ensure our research software serves everyone in our communities. That is why this program focuses on people who belong to groups that are historically and systematically excluded from the open software and research software communities and who are interested in contributing to rOpenSci and the broader open source and research software communities.

Become a Mentor for rOpenSci Champions!

Thu, 20 Oct 2022 00:00:01 -0700

rOpenSci is seeking mentors to support our inaugural cohort of rOpenSci Champions!

The rOpenSci Champions Program is for people from historically and systematically excluded groups who are interested in contributing to rOpenSci and the broader ecosystem of open source and open science communities. After receiving training, mentors will work with Champions to develop their project, which can be one of the following options:

Create a new package;
Go through the review process with an R package they have already developed;

Interesting Uses of censo2017 a Year After Publishing

Wed, 19 Oct 2022 00:00:00 +0000

Read it in: Español.

Summary

This post is about the surprising uses I’ve noticed and the questions about the censo2017 R package, a tool for accessing the Chilean census 2017 data, I’ve gotten since it was peer-reviewed through rOpenSci one year ago. The original post about the package one year ago didn’t cover the different examples I present here, including a Python port of the R package.

Organizing the census data

Three years ago, I had to complete an assignment that required me to extract data from Windows-only software in DVD format, which got very complicated.

rOpenSci. Open Source Software Community

Tue, 18 Oct 2022 15:00:00 +0000

Maintain or Co-Maintain an rOpenSci Package!

Mon, 17 Oct 2022 00:00:00 +0000

The rOpenSci suite of packages is mainly composed of packages contributed by the community through peer-review, but also includes some packages maintained by staff. Over time, the commitments and availability of the original developers of a package can change. This leads to some maintainers stepping down from their maintainer role, or other maintainers looking to lower their workload through more teamwork and therefore looking for co-maintainers.

We’re so grateful for all our community maintainers and want to make sure that they feel good about the work they do and not burdened by the responsibility. This is why we started conducting annual maintainer surveys, to ensure that maintainers feel supported and feel free to say when they need help, or are ready to move on. Following our recent annual maintainer survey, we have projects looking for both new maintainers and co-maintainers. Therefore, we say thank you! to our maintainers looking to move on, and in this blog post we will explain why you might want to help, and we’ll list the packages currently up for adoption or collaboration.

Backing up GitHub organisation with gitcellar

Wed, 12 Oct 2022 00:00:00 +0000

rOpenSci package or resource used*

gitcellar
blog post: Safeguards and Backups for GitHub Organizations

What did you do?

I replicated the back-up infrastructure from rOpenSci in our GitHub organisation: https://github.com/epiverse-trace.

Migration archives are created with gitcellar and are then uploaded to a DigitalOcean S3-compatible space with the aws.s3 R package.

This is automated via GitHub Actions and runs on a weekly basis (each Saturday in the night).

For increased security, I have created a dedicated GitHub account, @epiverse-trace-bot, which hosts the repository with the automation and also provides a Personal Access Token (PAT) with minimal permissions.

Social Coworking and Office Hours - Start writing that package!

Tue, 04 Oct 2022 03:00:00 +0000

Join us for 2 hours Tuesday, October 4th, 9 AM Australian Western / 1:00 UTC for
Social Coworking + Office Hours

This October we’re focusing on the theme Start writing that package! with community host Nick Tierney, R enthusiast and author of several R packages.

Come for the full 2 hrs or only as long as you need!

Using a targets pipeline to query data from the Water Quality Portal

Mon, 03 Oct 2022 00:00:00 +0000

rOpenSci package or resource used

targets dataRetrieval

What did you do?

We developed a reproducible pipeline to query data from the Water Quality Portal (WQP) based upon a user-specified area of interest. This template provides a framework for others to inventory, query, and then clean data from WQP.

Querying and cleaning data from the WQP based on an area of interest is a common data access pattern across many projects from USGS, so we developed a template repository that other users could fork and integrate into their project-specific workflows. The blog post goes into further detail about the “ins and outs” of this access pattern - focusing on the first two phases of the pipeline (01_inventory and 02_download) because these phases tend to be consistent across projects. In the GitHub repo we also include a few example cleaning functions that users can review and use to guide their own data cleaning methodologies.

rOpenSci News Digest, September 2022

Fri, 23 Sep 2022 00:00:00 +0000

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

We are thrilled to launch our Champions program!

rOpenSci Champions Program is part of a series of activities and projects we are carrying out to ensure our research software serves everyone in our communities. That is why this program focuses on people who belong to groups that are historically and systematically excluded from the open software and research software communities and who are interested in contributing to rOpenSci and the broader open source and research software communities.

Announcing the rOpenSci Champions Program!

Thu, 22 Sep 2022 00:00:01 -0700

Read it in: Español.

We are thrilled to launch our Champions Program pilot!

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. This disappointing lack of diversity is potentially detrimental to the sustainability, utility and productivity of projects.

Using handlr to convert bibtex citation to cff

Fri, 16 Sep 2022 00:00:00 +0000

rOpenSci package or resource used*

handlr

What did you do?

I was working on an R package with data to become publicly available. The data is already described and used in a scientific paper, and as such I had a bibtex citation I wanted to use as CITATION.cff on github. I was struggling to find a way to turn bibtex to cff, and asked on the forum if there were any tools to help. The citation has quite a lot of co-authors, so I didnt want to start writing all that by hand. I got an amazing reply and {handlr} seemed to be what I was looking for.

How to Participate with rOpenSci

Tue, 13 Sep 2022 00:00:01 -0700

Read it in: Español.

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! rOpenSci fosters a culture that values open and reproducible research using shared data and reusable software. We are dedicated to providing a welcoming and supportive environment for all people. By participating in this community, participants agree to abide by our Code of Conduct. Whether you have a little or a lot of time, there are many ways to contribute and engage with us.

Using taxize and highcharter in R to extract and visualize taxonomic data

Tue, 13 Sep 2022 00:00:00 +0000

rOpenSci package or resource used*

taxize

What did you do?

I used taxize to classify a list of endangered species and visualized the taxonomic hierarchical relationship via highcharter.

URL or code snippet for your use case*

R Script

Image

Sector

other

Field(s) of application

ecology, taxonomy

Social Coworking and Office Hours - Teaching with R

Tue, 06 Sep 2022 18:00:00 +0000

We’re back!

Join us for 2 hours Tuesday, September 6th, 9 AM North American Pacific / 16:00 UTC for Social Coworking + Office Hours

This September we’re focusing on the theme Teaching with R with our new community manager, Yanina Bellini Saibene, as co-host!

Come for the full 2 hrs or only as long as you need!

rOpenSci News Digest, August 2022

Fri, 26 Aug 2022 00:00:00 +0000

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

Coworking sessions resume!

Working with Qualtrics Data - Part 2: Excluding Data

Tue, 09 Aug 2022 00:00:00 +0000

In the last post, we used the qualtRics¹ package to import survey data directly from Qualtrics accounts. I often use Qualtrics for survey data collected via Amazon’s Mechanical Turk, which is an automated system that connects online respondents to paid surveys. However, sometimes those data are not super useful because the quality of the data is poor. In the anonymous, large-scale market of online survey respondents, the financial incentives for completing surveys attract respondents who blast through the study just to collect the money or, worse, automated bots programmed to act like humans and reap the incentives. 🤖 As a scientist, I’m collecting survey data to understand human nature, so I’m looking for honest responses. But low-quality data can be common in online surveys, and not just on Mechanical Turk².

Working with Qualtrics Data - Part 1: Importing Data

Tue, 02 Aug 2022 00:00:00 +0000

The online survey system Qualtrics can be a great way to collect data from research participants, customers, and stakeholders. I use it frequently to conduct research studies with participants or just to poll students and collaborators. However, while Qualtrics makes survey design straightforward, once the data are collected, there is a lot of work to do. Fortunately, two R packages (qualtRics¹ and excluder²) can make importing data and excluding low-quality data easier.

New Package yfR

Tue, 26 Jul 2022 00:00:00 +0000

Package yfR recently passed peer review at rOpenSci and is all about downloading stock price data from Yahoo Finance (YF). I wrote this package to solve a particular problem I had as a teacher: I needed a large volume of clean stock price data to use in my classes, either for explaining how financial markets work or for class exercises. While there are several R packages to import raw data from YF, none solved my problem.

rOpenSci News Digest, July 2022

Fri, 22 Jul 2022 00:00:00 +0000

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 Code of Conduct update

We are pleased to announce the release of a new version of our Code of Conduct.
Based on the feedback of our community we added greater detail about acceptable and unacceptable behaviors in online settings and we have the first translation of the text to Spanish.

Upgrading rtweet

Thu, 21 Jul 2022 00:00:00 +0000

In this post I will provide some examples of what has changed between rtweet 0.7.0 and rtweet 1.0.2. I hope both the changes and this guide will help all users. I highlight the most important and interesting changes in this blog post, and for a full list of changes you can consult it on the NEWS.

Big breaking changes

More consistent output

This is probably what will affect the most users. All functions that return data about tweets¹ now return the same columns.

rOpenSci Code of Conduct Update

Tue, 12 Jul 2022 00:00:00 +0000

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.

As always our Code of Conduct uses community sources to improve. For these changes, we have consulted and adapted the useR! 2021 Code of Conduct.

Evaluating GitHub Activity for Contributors

Fri, 01 Jul 2022 00:00:00 +0000

Read it in: Español.

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. 😉

rOpenSci News Digest, June 2022

Fri, 24 Jun 2022 00:00:00 +0000

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

Introducing rOpenSci new Community Manager, Yanina Bellini Saibene

We’re excited and extremely thrilled to announce Yanina Bellini Saibene is our new community manager! Yanina is a computer and data scientist by training and an educator by choice. She lives in Argentina, where she has been a researcher for the last 24 years. She is also a professor at Universidad Nacional Guillermo Brown. She is part of several communities as a member of The Carpentries Executive Council, R-Ladies Global and Leadership Team, R Forwards Core Team, R Consortium Infrastructure Steering Committee, useR! Working Group, Minorities in R (MiR), and Sociedad Argentina de Informática.

Introducing rOpenSci new Community Manager, Yanina Bellini Saibene

Tue, 21 Jun 2022 00:00:01 -0700

Read it in: Español.

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.

When I saw the call for the position, I thought that my over 20 years of experience as a community builder, teacher, and researcher aligned perfectly with it.

I believe in the power of open science at the service of people, that education is the best tool we have to improve lives, and that the most effective way to make changes is as part of a community. rOpenSci combines my passion for open software and open science with my favorite programming language and community. I am particularly excited by our new project to empower community leaders from historically excluded groups and looking forward to playing a role in its development. I have worked to improve diversity, equity, and inclusion throughout my career, both because I am a member of groups that are historically excluded from science and because it’s the right thing to do.

Why You Should (or Shouldn't) Build an API Client

Thu, 16 Jun 2022 00:00:00 +0000

These days web Application Programming Interfaces (APIs) are everywhere (scientific data sources, your system for Customer relationship management, cat facts API…). Do you need to write some R code wrapping a web resource such as an API? Packaging it up might be useful to you or your team for the same reason as any code. Now, whether you really want to publicize the package and to guarantee its maintenance might be slightly trickier than for other packages, as the usefulness and status of your package will depend on the web API being up and running according to expectations. This creates a surface for failures that might be more or less scary depending on your trust in the upstream maintainers.

Communication & Collaboration with Contributors in an Open-Source Organization

Tue, 14 Jun 2022 00:00:00 +0000

Zhiam Kamvar is Lesson Infrastructure Technology Developer at The Carpentries (Software Carpentry, Data Carpentry & Library Carpentry), an open global community teaching the skills & perspectives to turn data into knowledge.¹ Maëlle Salmon is a Research Software Engineer with rOpenSci. In this post they compare their experiences in the two distinct organizations The Carpentries and rOpenSci.

At rOpenSci, many packages are maintained by volunteer community members, and similarly at The Carpentries lessons are maintained by volunteer community members. We’re very thankful for the effort our volunteers put into that role and our organisations could literally not run without their work. However, sometimes infrastructure changes are decided centrally. For example, requiring two-factor authentication for all GitHub organization members at rOpenSci or overhauling the foundation of the lesson infrastructure at The Carpentries. In this post, we shall share some insights from our experiences regarding how we, as staff members, best support our volunteers through these transformations.

rOpenSci.Convertite en una campeona del desarrollo de paquetes de R

Fri, 10 Jun 2022 21:00:00 +0000

Reunión Argentina de Agrometeorología (Argentine Meeting of Agrometeorology)

Fri, 10 Jun 2022 13:00:00 +0000

WiDS La Plata

Fri, 10 Jun 2022 13:00:00 +0000

Canal de YouTube https://www.youtube.com/c/VideosUNLP

rOpenSci Dev Guide 0.8.0: Updates

Thu, 09 Jun 2022 00:00:00 +0000

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. The Dev Guide included several references to Stefanie, particularly regarding preparing blog posts, as well as preparing Dev Guide releases. Her name has been removed and replaced with a generic “Community Manager” title.

rOpenSci Software Peer Review, 🤗 Empathy, 📶 communication, 🗒️ documentation, and 🤖 automation

Tue, 07 Jun 2022 03:00:00 +0000

Social Coworking and Office Hours - Tackle something you've always wanted to learn

Tue, 07 Jun 2022 03:00:00 +0000

Join us for 2 hours Tuesday, June 7th, 9 AM Australian Western / 1:00 UTC for
Social Coworking + Office Hours

This June we’re focusing on the theme Tackle something you’ve always wanted to learn with community host Nick Tierney, R enthusiast and author of several R packages.

Come for the full 2 hrs or only as long as you need!

Map of linguae francae of Dagestan, Russia

Thu, 02 Jun 2022 00:00:00 +0000

rOpenSci package or resource used

lingtypology

What did I do?

There is a long tradition in linguistics of drawing polygons to delimit the areas in which languages are spoken. However, in typological studies in linguistics, a lot of languages need to be represented on maps, so the “one dot per language” approach is used. In multilingual areas with high language density like Dagestan (see the Multidagestan project (Dobrushina et al. 2017) that shows this), it is common for people to know more than one language, including linguae francae, i.e., languages used by speakers of different languages to communicate with one another. Nowadays, for all Post-Soviet states, the common lingua franca is Russian. However, historically, there were three linguae francae in Dagestan. Nina Dobrushina and I decided to create a map to show this old distribution of linguae francae. In order to do so, I used the dataset of East Caucasian villages (Moroz, Verhees 2020), which contains information about modern settlements of Dagestan with language attribution. Afterwards, I used the density.estimation argument from lingtypology, hid dots used in the extrapolation and overlayed with another map based on the “one dot per language” approach.

Editorial Automation: Why & How to Set Up Chat-Ops for your Own Review System on GitHub

Tue, 31 May 2022 00:00:00 +0000

Anyone can contribute a software package to the rOpenSci suite as long as it fits our scope (research lifecycle software and statistical software) for a transparent, constructive, nonadversarial and open review. In practice, the review steps are all recorded in GitHub issue threads (example). Software peer-review involves coordinating and tracking many moving parts: software submissions (new issues), testing and diagnostics, assignment of editors and reviewers, and logging the progression of submissions through revisions and acceptance.

Extração de dados sobre heróis negros e negras da Marvel e DC

Mon, 30 May 2022 00:00:00 +0000

rOpenSci package or resource used*

tabulizer [pt-br]

What did you do?

Uso do tabulizer para extrair dados sobre heróis negros e negras da DC e Marvel disponibilizados em uma tabela de uma dissertação disponibilizada em arquivo pdf.

URL or code snippet for your use case*

https://github.com/fernandobarbalho/herois_negros_negras

rOpenSci News Digest, May 2022

Fri, 20 May 2022 00:00:00 +0000

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 prominently displays more information on packages!

We have extended the r-universe.dev platform to provide even more real-time information and metadata about R packages to help users quickly find and compare relevant software for a given topic, maintainer or organization.

Requiring 2FA for Our Main GitHub Organization

Mon, 16 May 2022 00:00:00 +0000

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 2023. Here is how (and why) we went about it.

Analyze your Twitter timeline with rtweet and lubridate

Sat, 14 May 2022 00:00:00 +0000

rOpenSci package or resource used*

https://github.com/correlaid/kbtbr

What did you do?

In this blog post I give a quick tour of the rtweet and lubridate package. These help you to analyse your Twitter timeline. And they helped me to visualize my follower count as I reached 1000 followers this week.

URL or code snippet for your use case*

Find my blog post at albert-rapp.de.

Image

Here’s a visual I created using the data I extracted the data from Twitter over time. It was a celebratory dataviz as I reached 1000 followers.

Social Coworking and Office Hours - Why be an R package reviewer?

Tue, 03 May 2022 18:00:00 +0000

Join us for 2 hours Tuesday, May 3rd, 9 AM North American Pacific / 16:00 UTC for
Social Coworking + Office Hours

This May we’re focusing on the theme Why be an R package reviewer? with community host François Michonneau, reviewer for rOpenSci Software Peer Review, Senior Director of Technology at The Carpentries, as well as maintainer of rOpenSci package rotl.

Don't Lose your HEAD over Default Branches

Fri, 29 Apr 2022 00:00:00 +0000

Did you know that GitHub lets you refer to the default branch of any repository by substituting the branch name with HEAD in the url? This is a very useful trick to write robust code that works regardless of whether the default branch is called main or master, and will keep working when the default branch gets renamed at some point.

While git has no “default” branch, online code platforms such as GitHub need to define a default for the branch that someone sees when they look at code online. While the community standard for the default branch is now becoming main instead of master¹, and while the switch for any repo is rather easy and is well supported by usethis, for a while (forever) there will still be repos with different default branches in the wild.² Especially as nothing prevents you from using any other name for the default branch (although this could trip up collaborators).³

rOpenSci News Digest, April 2022

Fri, 22 Apr 2022 00:00:00 +0000

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

pkgcheck reports now include dependencies

Our automated checking system for packages submitted for peer review now has a new section, “Package Dependencies”. This is intended to help editors and reviewers understand how package dependencies (that is, packages listed in Imports, Depends, or Suggests DESCRIPTION fields) are actually used by a package. The section summarises total numbers of function calls made to each package, followed by collapsible “details” sections containing numbers of calls made to the individual functions of each packages. Dependencies include base R and all recommended packages, ensuring that this section provides a comprehensive overview of how each package submitted for peer review uses and depends upon the entire R ecosystem.

Estimating leaf temperatures worldwide

Thu, 21 Apr 2022 00:00:00 +0000

rOpenSci package or resource used*

nasapower.

What did you do?

As a plant pathologist, I am interested in improving the characterisation of environmental influences on pathogen infection. This piqued my interest if there are any R packages that estimate leaf temperatures and/or humidity from ambient weather variables. A cursory search led me to the tealeaves.

However, the tealeaves package requires additional parameters which are not logged by common weather stations, such as short wave solar radiation and albedo. However, I was aware that nasapower provides all the weather inputs required on a 0.5 degree grid from satellite remote sensing.

Editorial Challenges and Solutions in Software Peer Review

Tue, 19 Apr 2022 00:00:02 -0700

Read it in: Español.Read it in: Português.

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. (Their role, like much of our process, is codified in the rOpenSci Developer Guide). While many in our community have participated in the peer-review process, only a few have been involved as editors and guest editors. Here we thought we’d shed some light on some of challenges our editors face, and some of the solutions we have found over the years, to make this part our work more transparent.

Social Coworking and Office Hours - Making figures sparkle

Tue, 05 Apr 2022 03:00:00 +0000

Join us for 2 hours Tuesday, April 5th, 9 AM Australian Western / 1:00 UTC for
Social Coworking + Office Hours

This April we’re focusing on the theme Making figures sparkle with community host Nick Tierney, author of several data visualization packages using ggplot2, including visdat with rOpenSci, and naniar.

Come for the full 2 hrs or only as long as you need!

rsnps 0.5.0: New ncbi_snp_query() Features

Tue, 29 Mar 2022 00:00:00 +0000

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. Previously (version <= 0.4.0), it reported only the allele frequency from gnomAD in column maf as a data.frame.

Using vcr for HTTP testing of a package for Kobotoolbox

Thu, 24 Mar 2022 00:00:00 +0000

rOpenSci package or resource used*

vcr
the excellent http testing in r book

What did you do?

We - a couple of volunteers from data4good network CorrelAid developed a wrapper for the API of Kobotoolbox, a data collection tool widely used in humanitarian aid. For testing the package functions, we used the vcr package and the HTTP testing book.

URL or code snippet for your use case*

Disclaimer: while we were developing, another package for the exact same purpose was published which is maybe better than ours (e.g. it uses labelled to store question labels as well): https://gitlab.com/dickoa/robotoolbox :)

Searching and browsing the R universe

Wed, 23 Mar 2022 00:00:00 +0000

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. Give it a try and search for any topic, author, or organization!

Safeguards and Backups for GitHub Organizations

Tue, 22 Mar 2022 00:00:00 +0000

At rOpenSci, much of our code, content and infrastructure is hosted on GitHub over several organizations – described on our resources page. This post summarizes some steps we’ve taken to safeguard our GitHub organizations.

Paying attention to access rights & individual security setup

GitHub defines several possible roles for organizations. The principal ones are:

Organization owners who have all rights;
Organization members who only have basic rights and access to specific repositories (more on that later!);
Outside collaborators who only have access to specific repositories.

To decide what role to give someone we use the principle of least privilege – obviously balanced with trust… and some consideration of the bus factor. We want everyone to be able to do their job (for instance, accessing all repo settings), to have more than one person able to perform something (in case of vacation and other vacancy reasons), but we do not want to give people unnecessary access to sensitive settings and information.

rOpenSci News Digest, March 2022

Fri, 18 Mar 2022 00:00:00 +0000

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

You can read this post on our blog. Now let’s dive into the activity at and around rOpenSci!

rOpenSci HQ

R-universe gets advanced search!

The landing page for rOpenSci’s R-universe platform has gotten a makeover to facilitate easy searching through thousands of available R packages and articles. Discover new content by searching for keywords in package descriptions, authors, topics, vignettes, etc.

Social Coworking and Office Hours - Changing package maintainers

Tue, 01 Mar 2022 19:00:00 +0000

Join us for 2 hours Tuesday, March 1st, 9 AM North American Pacific / 17:00 UTC for
Social Coworking + Office Hours

This March we’re focusing on the theme Changing package maintainers with community host Hannah Owens, who recently took over maintenance of the rOpenSci spocc package.

Come for the full 2 hrs or only as long as you need!

Use rtweet to manage lists and who you follow

Tue, 22 Feb 2022 00:00:00 +0000

rOpenSci package or resource used*

What did you do?

After capturing a list of the people you follow, this workflow enables you to:

assign twitter accounts to different groups (e.g. via RegEx over the profile)
use the group boolean columns as the basis to create and populate lists*
mass un-follow people so that your core twitter feed is streamlined

* I noticed significant instability in the Twitter list APIs. A workaround (that was still a bit flaky!) is to split the accounts into groups of 100 and use Tweetdeck to bulk add people to lists. The spit() function in the gist is how I tackled this.

rOpenSci News Digest, February 2022

Fri, 18 Feb 2022 00:00:00 +0000

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 is hiring its next Community Manager!

Come be part of making our great community even better;
Help start a new program promoting diverse leadership in open source;

A Journey to gghdr

Tue, 15 Feb 2022 00:00:00 +0000

They may forget what you said, but they will never forget how you made them feel.

Carl W. Buehner

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. The highest density region approach of summarizing a distribution is useful for analyzing multimodal distributions and can be composed of numerous disjoint subsets. For example, the histogram of the highway mileage (hwy) data from the mpg dataset (a) shows that cars with 6 cylinders (cyl) are bimodally distributed, which is reflected in the highest density region (HDR) boxplot (c) but not in the standard boxplot (b). Hence, we see that HDRs are useful in displaying multimodality in the distribution.

Calculating US Residential Segregation Indices in A Reproducible Pipeline

Fri, 11 Feb 2022 00:00:00 +0000

We provide a simple and reproducible R pipeline to investigate residential segregation (RS) using US census data. The pipeline contains two components:

pulling decennial US census data of Year 2000, 2010, 2020 via R package tidycensus
calculating three residential segregation indices, including dissimilarity, isolation and interaction indices, at the preferred geographical level, e.g. county or census tract level

rOpenSci package or resource used*

What did you do?

We pull decennial US census data with tidycensus and calculate three residential segregation indices.

Social Coworking and Office Hours

Tue, 01 Feb 2022 03:00:00 +0000

Join us for 2 hours Tuesday, February 1st, 9 AM Australian Western / 1:00 UTC for Social Coworking + Office Hours.

We are hosting Social Coworking + Office Hours on the first Tuesday of each month, alternating times to accommodate different parts of the world.

Come for the full 2 hrs or only as long as you need!

Meet other package developers and rOpenSci staff in Zoom
Cowork independently on work related to R
- Plan out that package you’ve always wanted to create
- Work on packages that tend to be neglected
- Make your packages more contributor-friendly (create issues, write a road map, etc.)
- What ever you need to get done!
Get answers to your questions
- Ask rOpenSci staff
- Ask your fellow developers
- Discuss your work, best practices, or get advice and resources
Answer other developers questions!

pkgcheck now available as a GitHub action!

Tue, 01 Feb 2022 00:00:00 +0000

Read it in: Español.Read it in: Português.

What is pkgcheck?

The pkgcheck package has been developed by rOpenSci to automate the process of checking all packages on submission. The ropensci-review-bot automatically runs pkgcheck on all submissions, and checks can also be called at any time by editors using the command:

@ropensci-review-bot check package

The bot will return a list of checks which should ideally look like this:

To be ready for peer review, pkgcheck should return a series of ✔, indicating successful checks, and there shouldn’t be any ✘ symbols, which indicate failed checks. Anybody preparing a package to submit is recommended to “use pkgcheck” to confirm that a package is indeed ready to submit. Until now, this has only been possible through locally installing the package and running the pkgcheck() command. Local checks suffer two important disadvantages:

A Blend of Package Build Failures

Mon, 31 Jan 2022 00:00:00 +0000

The rOpenSci R-universe is a bit special as, compared to other R-universes, it builds docs for all the packages in our suite. Looking at the dashboard helps us identify failures in building the packages as well as in building the pkgdown websites. We then help authors fix these issues in order to comply with our package curation policy. As a package author you should also rely on continuous integration in your own repo for catching e.g. R CMD check problems. Following one of our latest rounds of monitoring, we summarize some common and less common mistakes. Many of them are not specific to our build system.

rOpenSci News Digest, January 2022

Fri, 21 Jan 2022 00:00:00 +0000

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

Co-working events

Join us for social coworking & office hours monthly on 1st Tuesdays! Hosted by Steffi LaZerte and Nick Tierney. Everyone welcome. No RSVP needed. Consult our Events page to find your local time and how to join.

Community Management Transition for rOpenSci. A Message from Stefanie Butland

Fri, 14 Jan 2022 00:00:00 +0000

I’m writing to share news that I’m moving on from my position as rOpenSci’s Community Manager. Friday, January 14th is my last day. Being rOpenSci’s first Community Manager has been my dream job. You have all given me such joy over the past 5.5 years. I love collaborating to create new things, so it’s time for me to step away and take some time to explore what might come next.

rOpenSci 2021 Code of Conduct Transparency Report

Thu, 13 Jan 2022 00:00:00 +0000

rOpenSci Code of Conduct Annual Review

Thu, 13 Jan 2022 00:00:00 +0000

Gather on the rOpenSci Forum

Tue, 11 Jan 2022 00:00:00 +0000

Do you have an account on the rOpenSci forum? As underlined in our contributing guide, our forum is where we encourage Q&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 easier for you to find where to post, and what to follow. In this post we shall present current forum categories, and ways for you to keep up-to-date with the activity without getting overwhelmed.

How renv restores packages from r-universe for reproducibility or production

Thu, 06 Jan 2022 00:00:00 +0000

What is renv

RStudio’s renv package is a powerful dependency management toolkit for R. It allows you to create a lockfile that records the exact versions of R packages used in a given project, and provides tooling to install exactly those same versions on another machine, or at a later point in time. This is very useful to create an isolated project environment for reproducibility or production purposes.

The latest version of renv (0.15.0) now supports restoring packages that were installed from r-universe. In this post we explain how this works, and why it has to work this way.

Social Coworking and Office Hours

Tue, 04 Jan 2022 19:00:00 +0000

Join us for 2 hours Tuesday, January 4th, 9 AM North American Pacific / 17:00 UTC for Social Coworking + Office Hours.

We are hosting Social Coworking + Office Hours on the first Tuesday of each month, alternating times to accommodate different parts of the world.

Come for the full 2 hrs or only as long as you need!

Meet other package developers and rOpenSci staff in Zoom
Cowork independently on work related to R
- Plan out that package you’ve always wanted to create
- Work on packages that tend to be neglected
- Make your packages more contributor-friendly (create issues, write a road map, etc.)
- What ever you need to get done!
Get answers to your questions
- Ask rOpenSci staff
- Ask your fellow developers
- Discuss your work, best practices, or get advice and resources
Answer other developers questions!

rOpenSci Announces $400k Award from the Chan Zuckerberg Initiative to Empower Historically Excluded Groups as Community Leaders in Scientific Open Source Projects

Mon, 20 Dec 2021 00:00:00 +0000

We are thrilled to have been awarded new funding as part of the Chan Zuckerberg Initiative Open Science program’s education and capacity building strategy. This $400K grant will support a new project to enable more members of historically excluded groups to participate in, benefit from, and become leaders in the R, research software engineering, and open source and open science communities.

Developers in the R and open source communities are overwhelmingly white, male, from a handful of countries, primarily English-speaking, and do not use assistive technologies to participate. Research software should serve everyone in our communities. It needs to be sustainable and open and built by and for all groups.

Thank You to the rOpenSci Community, 2021

Fri, 17 Dec 2021 00:00:00 +0000

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?

Consider leaving them a note in the comments below expressing your gratitude. We often think our thank yous, but expressing thank yous can be incredibly meaningful. Try to be specific. What did they do? What impact did their actions have?

Enhancing Software Peer Review with GitHub Automation

Tue, 02 Nov 2021 00:00:00 +0000

Software peer-review involves coordinating and tracking many moving parts: software submissions, testing and diagnostics, assignment of editors and reviewers, and logging the progression of submissions through revisions and acceptance.

On this call we will discuss how rOpenSci has worked with The Journal of Open Source Software to extend JOSS’s approach of chatops-driven publishing into a new GitHub chat-bot that manages our editorial process: assigning tasks, tagging issues, running tests on software submissions, and returning reports to reviewers and editors, logging reviews in an external (Airtable) database, all from the comfort of a GitHub issue comment. Chat-ops automation has been critical to JOSS’s success, and shows huge promise for automating even more tedious tasks like frequent software checks and compliance with best practices.

Social Coworking and Office Hours

Tue, 07 Dec 2021 03:00:00 +0000

Join us for 2 hours Tuesday, December 7th, 9 AM Australian Western / 1:00 UTC for Social Coworking + Office Hours.

We are hosting Social Coworking + Office Hours on the first Tuesday of each month, alternating times to accommodate different parts of the world.

Come for the full 2 hrs or only as long as you need!

Meet other package developers and rOpenSci staff in Zoom
Cowork independently on work related to R
- Plan out that package you’ve always wanted to create
- Work on packages that tend to be neglected
- Make your packages more contributor-friendly (create issues, write a road map, etc.)
- What ever you need to get done!
Get answers to your questions
- Ask rOpenSci staff
- Ask your fellow developers
- Discuss your work, best practices, or get advice and resources
Answer other developers questions!

Evaluating semi-parametric nowcasts of COVID-19 hospital admissions in Germany

Tue, 30 Nov 2021 00:00:00 +0000

rOpenSci package or resource used

targets, piggyback

What did you do?

COVID-19 hospitalisations in Germany are released by date of positive test rather than by date of admission. This has some advantages when they are used as a tool for surveillance as these data are closer to the date of infection and so easier to link to underlying transmission dynamics and public health interventions. Unfortunately, however, when released in this way the latest data are right-censored meaning that final hospitalisations for a given day are initially underreported. This issue is often found in data sets used for the surveillance of infectious diseases and can lead to delayed or biased decision making. Fortunately, when data from a series of days is available we can estimate the level of censoring and provide estimates for the truncated hospitalisations adjusted for truncation with appropriate uncertainty. This is usually known as a nowcast.

rOpenSci News Digest, November 2021

Tue, 30 Nov 2021 00:00:00 +0000

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: @ropensci-review-bot help!

Tuesday, 07 December 2021 17:00 UTC we’ll share how we are Enhancing Software Peer Review with GitHub Automation.

Speakers Arfon Smith, Karthik Ram, Maëlle Salmon and Noam Ross will discuss how rOpenSci has worked with The Journal of Open Source Software (JOSS) to extend their approach of chatops-driven publishing into a new GitHub chat-bot that manages our editorial process: assigning tasks, tagging issues, running tests on software submissions, and returning reports to reviewers and editors, all from the comfort of a GitHub issue comment. Chat-ops automation has been critical to JOSS’s success, and shows huge promise for automating even more tedious tasks like frequent software checks and compliance with best practices. We will show how our new review bot improves the author and editor experience, explain how other teams can use and customize the bot, and discuss how this approach can be extended to tackle other automation, code review, and reproducibility challenges.

RSS feeds of package updates in r-universe

Wed, 24 Nov 2021 00:00:00 +0000

Continuous deployment in r-universe

A major difference between r-universe and static repositories like CRAN and BioConductor is continuous deployment: packages in r-universe are continuously built in CI and immediately deployed to our package server. This package server stores binaries and metadata in a database, which enables us to dynamically query and expose all the package data through APIs, dashboards, feeds, etc.

The package server also makes it relatively easy to add new functionality to expose information about R packages from the database in some other way. For example, we recently added a badges API to display package versions and totals in the form of a small badge image that can be embedded in webpages.

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

Tue, 23 Nov 2021 00:00:00 +0000

A new R package, cffr, has been developed, peer-reviewed by rOpenSci and accepted by CRAN. This package has a single purpose: to create a valid CITATION.cff file using the metadata of any R package.

CITATION.cff files and why they matter

A Citation File Format (CFF) is a plain text file with human- and machine-readable citation information for software (and datasets)¹.

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

Tue, 23 Nov 2021 00:00:00 +0000

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

I borrowed some ideas from codemetar, although I decided to create most of my code from scratch (I enjoy challenging myself, and there is no better way of learning). Finally, the first working version of cffr was released on September 15, 2021.

rOpenSci Dev Guide 0.7.0: Updates

Thu, 18 Nov 2021 00:00:00 +0000

rOpenSci Software Peer Review’s guidance is gathered in an online book and keeps improving! To find out what’s new in our dev guide 0.7.0, you can read the changelog, or this blog post for more digested information.

@ropensci-review-bot help: less TODOs, more simple commands!

A big change brought in this release is the retirement of some of our multiple TODOs for editors in favor of simple bot commands such as @ropensci-review-bot check package. Our editor guide is now simpler!

How to Cite R and R Packages

Tue, 16 Nov 2021 00:00:00 +0000

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.

Many scientists don’t know that they should be citing R packages let alone R, and, if they do know, they often struggle with how. So here’s a short primer on why and how to get started!

Jeroen Ooms on The r-universe at NHS-R Conference

Tue, 09 Nov 2021 16:25:00 +0000

Jeroen Ooms, rOpenSci Lead Infrastructure Engineer will give a talk on The r-universe project at the NHS-R 2021 virtual conference.

NHS is the UK National Health Service and the NHS-R community “aims to support the learning, application and exploitation of R in the NHS through workshops, video tutorials and providing a platform for discussion and sharing of developing best practice solutions to NHS problems.”

Conference program.

Social Coworking and Office Hours

Tue, 02 Nov 2021 18:00:00 +0000

Join us for 2 hours Tuesday, November 2nd, 9 AM Pacific / 16:00 UTC for Social Coworking + Office Hours.

We are hosting Social Coworking + Office Hours on the first Tuesday of each month, alternating times to accommodate different parts of the world.

Come for the full 2 hrs or only as long as you need!

Meet other package developers and rOpenSci staff in Zoom
Cowork independently on work related to R
- Plan out that package you’ve always wanted to create
- Work on packages that tend to be neglected
- Make your packages more contributor-friendly (create issues, write a road map, etc.)
- What ever you need to get done!
Get answers to your questions
- Ask rOpenSci staff
- Ask your fellow developers
- Discuss your work, best practices, or get advice and resources
Answer other developers questions!

Expanding Software Peer Review: Statistical Package Standards at rOpenSci

Mon, 18 Oct 2021 00:00:00 +0000

This is the second in a series of 1-hour Community Calls on our statistical software review project.

We at rOpenSci have expanded the scope of our software peer review system to encompass explicitly statistical software. The first Community Call in this series covered new tools to help people prepare their software for submission. This time, we will address the bigger picture of how our community-informed development of standards for statistical packages meets a critical need of stakeholders. Noam Ross (EcoHealth Alliance and rOpenSci Software Review Lead) will catch everyone up on the project. Rebecca Killick (Lancaster University and rOpenSci Statistical Software Peer Review advisory committee) will offer insights into standardisation and the potential role our program might play in the future of statistical software and open source software in general. Juliane Manitz (EMD Serono and R Validation Hub) will offer a perspective on the use of open source software in regulated environments. Christoph Sax (cynkra) will share his experience as the first person to submit a package, tsbox, for review and aligning his software with our standards.

rOpenSci News Digest, October 2021

Fri, 22 Oct 2021 00:00:00 +0000

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 about the statistical software review project

A fantastic community call is coming up on Tuesday, 26 October 2021 18:00 UTC: Expanding Software Peer Review: Statistical Package Standards at rOpenSci!

Generating and customizing badges in r-universe

Thu, 14 Oct 2021 00:00:00 +0000

Read it in: Español.Read it in: Português.

Badges in r-universe

After creating your personal universe, the dashboard on https://{yourname}.r-universe.dev shows the version and other details for each package in your repository. We have also added a new tab that lists the available badges for the repository.

Badges provide a nice way to display the status of your repository or individual packages within external webpages, such as a README file, your homepage, or your personal or organization profile README on GitHub.

Predizendo volume de eucalipto com tidymodels, XGBoost e targets

Wed, 13 Oct 2021 00:00:00 +0000

rOpenSci package or resource used*

What did you do?

Neste tutorial, realizei o ajuste de diversos modelos de Machine Learning para a predição do volume de madeira de Eucalyptus. De modo geral, foi realizado o ajuste de diversos modelos, então foi feito o ajuste final e a avaliação da qualidade preditiva do melhor modelo obtido. Em seguida, realizou-se o orquestramento de todo o trabalho, a partir do pacote targets, bem como a produção automática de um relatório final com o resultado da modelagem.

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

Tue, 12 Oct 2021 00:00:00 +0000

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

rOpenSci has been running a rigorous and collegial software peer review system since 2015. Editors manage the review process, performing initial package checks, identifying reviewers, and moderating the process until the package is accepted by reviewers and transferred to rOpenSci. To address the scope and volume of packages submitted for review, it’s critical that we have a team of editors with complementary expertise. Adam brings his broad experience with API packages and his experience from agricultural research in academia, an international non-government organisation and government. Emily is known for openly sharing her processes-oriented approach to development based in her experience in industry. Jeff works hard at expanding open source tooling and skills in environmental science, particularly in government.

Creating historical Congressional maps with USABoundaries

Sun, 10 Oct 2021 00:00:00 +0000

rOpenSci package or resource used

USAboundaries

What did you do?

While reading a book about a futile presidential candidacy in the 1800s by Mormon leader Joseph Smith, I noticed that he proposed radically reshaping congressional apportionment rules and only assigning one House Representative per 1 million residents per state. I wanted to see what that would have done to Congress in the 1840s, and I wanted to make a map showing how many representatives each state would get under the proposed rules.

Social Coworking and Office Hours

Tue, 05 Oct 2021 03:00:00 +0000

Join us for 2 hours Tuesday, October 5th, 9 AM Australian Western / 1:00 UTC for Social Coworking + Office Hours.

We are hosting Social Coworking + Office Hours on the first Tuesday of each month, alternating times to accommodate different parts of the world.

Come for the full 2 hrs or only as long as you need!

Meet other package developers and rOpenSci staff in Zoom
Cowork independently on work related to R
- Plan out that package you’ve always wanted to create
- Work on packages that tend to be neglected
- Make your packages more contributor-friendly (create issues, write a road map, etc.)
- What ever you need to get done!
Get answers to your questions
- Ask rOpenSci staff
- Ask your fellow developers
- Discuss your work, best practices, or get advice and resources
Answer other developers questions!

Using jsonvalidate to validate the packages.json file from your personal universe

Tue, 05 Oct 2021 00:00:00 +0000

rOpenSci package or resource used*

jsonvalidate (and R-universe)

What did you do?

Use the jsonvalidate package to validate the contents of packages.json against a schema in your personal R-universe. This can be part of a GitHub Action set up to run on pull requests to ensure you only merge correctly formatted changes.

URL or code snippet for your use case*

schema.json:

{
"$schema": "http://json-schema.org/draft-07/schema#",
"title": "r-universe packages.json",
"description": "A packages.json file controlling the contents of your r-universe",
"type": "array",
"items": {
"type": "object",
"properties": {
"package": {
"description": "The name of the R package",
"type": "string"
},
"url": {
"description": "The URL to the git repository with the package source code",
"type": "string",
"format": "uri"
},
"subdir": {
"description": "A subfolder of the repository containing the R package",
"type": "string"
},
"branch": {
"description": "The branch from which the package should be built",
"type": "string"
}
},
"required": ["package", "url"]
}
}

.github/workflows/validate-json.yaml:

rOpenSci News Digest, September 2021

Thu, 30 Sep 2021 00:00:00 +0000

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!

The Story Behind rspatialdata

Tue, 28 Sep 2021 00:00:00 +0000

As two postgrad students on summer vacation but with no travel plans (during this global pandemic of course), we took up an internship at King Abdullah University of Science and Technology (KAUST) last summer and ended up collaborating on a really cool project with Paula Moraga! Did we mention that we worked in Saudi Arabia, while living in Australia? All is well when we have the internet.

We also ended up presenting our project at useR! 2021, and winning an award for the most outstanding lightning talk! So, keep reading to see how we got there!

ASA-BIOP 2021 conference

Fri, 24 Sep 2021 16:00:00 +0000

Abstract: rOpenSci is currently expanding its system for peer-review of R packages to include packages implementing statistical algorithms. This talk will briefly present two new tools developed for our expansion of scope, in order to assess statistical packages. The first, the “autotest” package, automatically generates and executes tests on R packages by determining the types of each input parameter for each function, and then mutating both types and values. This can be used to document and confirm the robustness of software to unexpected inputs. The second tool, the “ssr” package, allows standards compliance to be integrated directly into R package code. Developers use a roxygen-like system to annotate code to record where and how specific standards standards are addressed, as well as providing context or explanation for non-compliance. The integration of standards within the code itself enables the automatic generation of detailed, explicit, and cross-linked reports on standards compliance.

Using stplanr to find shortest road network distance to a TB treatment clinic from a TB patients' household.

Mon, 20 Sep 2021 00:00:00 +0000

rOpenSci package or resource used*

stplanr

What did you do?

We estimated the distance from study participants’ (TB patients) households to their TB treatment initiation clinic using two approaches. The first approach was to estimate the distance based on a ‘straight line’ distance Cartesian distance. In the second approach, we used Blantyre urban road network downloaded from OpenStreetMap (OpenStreetMap Foundation) to calculate the shortest road network distance using the stplanr R package

How to Use System Commands in your R Script or Package

Mon, 13 Sep 2021 00:00:00 +0000

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 package.

Social Coworking and Office Hours

Tue, 07 Sep 2021 18:00:00 +0000

Join us for 2 hours Tuesday, September 7th, 9 AM Pacific / 16:00 UTC for our first official Social Coworking + Office Hours event.

We are hosting Social Coworking + Office Hours on the first Tuesday of each month, alternating times to accommodate different parts of the world.

Come for the full 2 hrs or only as long as you need!

Meet other package developers and rOpenSci staff in Zoom
Cowork independently on work related to R
- Plan out that package you’ve always wanted to create
- Work on packages that tend to be neglected
- Make your packages more contributor-friendly (create issues, write a road map, etc.)
- What ever you need to get done!
Get answers to your questions
- Ask rOpenSci staff
- Ask your fellow developers
- Discuss your work, best practices, or get advice and resources
Answer other developers questions!

Slicing an image with magick for artistic effect

Tue, 07 Sep 2021 00:00:00 +0000

rOpenSci package or resource used

https://github.com/gkaramanis/aRtist/tree/main/mitosis

What did you do?

I used magick to slice an image and combine the tiles created to recreate the effect seen in Mario Klingemann’s work “Mitosis”

Image

Code and more images

Field(s) of application

Art

rOpenSci docs are now built on r-universe

Fri, 03 Sep 2021 00:00:00 +0000

TLDR: As of today, the pkgdown sites for all rOpenSci packages on our docs server are built on r-universe. This is an internal change; no action is required for package maintainers.

From Jenkins to r-universe

For the past 2 years we have been using a Jenkins server to automatically build the pkgdown sites for all rOpenSci packages, which get published on https://docs.ropensci.org. By centralizing this process, we ensure that up-to-date documentation for all rOpenSci packages is available from a consistent URL with our personal branding, and without maintenance work for our package maintainers.

Bayesian Regression Analysis with Rstanarm (with GSODR for supporting data)

Thu, 02 Sep 2021 00:00:00 +0000

Spotted in the wild. GSODR was used to provide the average daily temperature in degrees Celsius and the total daily precipitation in millimetres for this blog post.

rOpenSci package or resource used

GSODR

What did you do?

I just read the blog post, but the author used GSODR to fetch weather data to demonstrate the use of Rstanarm for Bayesian regression analysis.

URL or code snippet for your use case

https://methodmatters.github.io/steps-bayesian-rstanarm/

rOpenSci News Digest, August 2021

Tue, 31 Aug 2021 00:00:00 +0000

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

You can read this post on our blog. Now let’s dive into the activity at and around rOpenSci!

rOpenSci HQ

Recordings of useR! 2021

Recordings of useR! 2021 are now available on the conference website.

You can watch contributions by rOpenSci staff:

Jeroen Ooms’ keynote talk about the R-universe project (slidedeck);

rOpenSci Introduces Monthly Social Coworking and Office Hours

Tue, 17 Aug 2021 00:00:00 +0000

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

Coworking is a great way to be productive and reduce feelings of social isolation (especially important over the last year)!

These sessions will give you the opportunity to

Meet other package developers and rOpenSci staff
Cowork independently on work related to R (and perhaps focus on work that often gets neglected)
Get answers to your questions

We will host sessions on the first Tuesday of each month, alternating times to accommodate different parts of the world. Come for the full 2 hrs or only as long as you need!

rOpenSci staff at joint AOS & SCO-SOC meeting 2021

Fri, 06 Aug 2021 15:30:00 +0000

Steffi LaZerte, rOpenSci’s Community Assistant, organized a lightning symposium “Great R packages for ornithologists” for this years joint meeting of the American Ornithological Society and Society for Canadian Ornithologists. Steffi starts the symposium rolling with a 5-min presentation, “How can ornithologists find R packages?”

Mark Padgham, rOpenSci Software Research Scientist, is also contributing to this lightning symposium with a 5-min presentation on an rOpenSci package, “osmdata: Roadless areas and avian diversity”.

rOpenSci at Ecological Society of America ESA 2021

Fri, 06 Aug 2021 04:00:00 +0000

Steffi LaZerte, rOpenSci’s Community Assistant, and Carl Boettiger, rOpenSci Advisor, are both talking at the Ecological Society of America’s annual meeting, August 2 - August 6, 2021.

Presentations will be available online for registrants to view, see live discussions scheduled below.

Steffi LaZerte

Title: “Using rOpenSci packages to access open data for ecology"
Inspire Session 6: “Open Data Resources During a Global Pandemic”
Live Discussion: Tuesday, August 3, 2021, 11:00 AM - 12:00 PM Pacific; 18:00 UTC; Find your local time

Informal package review using rOpenSci review template

Wed, 04 Aug 2021 00:00:00 +0000

rOpenSci package or resource used*

Review template from the package development guide

Bonus: gert to automatically retrieve the hash of the commit of the reviewed version (gert::git_commit_id())

What did you do?

Informal package review for teammates before submission to a journal.

URL or code snippet for your use case*

https://github.com/epiforecasts/scoringutils/issues/121

Sector

academic

Field(s) of application

epidemiology

Answering 'what colour is London?' with magick and rtweet

Tue, 27 Jul 2021 00:00:00 +0000

rOpenSci package or resource used

What did you do?

I used rtweet to extract the images and body text (containing coordinates) from tweets by @londonmapbot, a bot that tweets satellite images of random parts of London (disclaimer: I made the bot). Then I used magick to simplify each image to a single colour and extract its hex value. I used this information to create some visualisations of ’the colour of London'.

The Story Behind censo2017, the First rOpenSci Package to be Reviewed in Spanish

Tue, 27 Jul 2021 00:00:00 +0000

Read it in: Español.

Summary

censo2017 is an R package designed to organize the Redatam¹ files provided by the Chilean National Bureau of Statistics (Instituto Nacional de Estadísticas de Chile in spanish) in DVD format². This package was inspired by citesdb (Noam Ross, 2020) and taxadb (Carl Boettiger et al, 2021). This post is about this package, the problem it solves, how to use it, and the fact that the package and its review process were all in Spanish.

Investigating the drought in the Canadian prairies

Mon, 26 Jul 2021 00:00:00 +0000

rOpenSci package or resource used*

https://github.com/alex-koiter/curiosity

What did you do?

Much of the Canadian prairies is experiencing drought conditions (https://agriculture.canada.ca/en/agriculture-and-environment/drought-watch-and-agroclimate/canadian-drought-monitor) resulting in significant wildfires and impacting agricultural production. I wanted to provide historical context for the current weather conditions.

URL or code snippet for your use case*

Image

Sector

academic, agriculture

Field(s) of application

Weather, climate, agriculture, disaster

targets pipeline with RMarkdown to download and visualize USGS data

Mon, 26 Jul 2021 00:00:00 +0000

rOpenSci package or resource used*

What did you do?

I was looking for a simple way to share code for a unique figure of cartogram bar charts related to the frequency of “ice” flags in public U.S. Geological Survey (USGS) streamgage data.

I could have written a regular script but I needed the code to download a lot of data for all 50 U.S. states. These downloads can sometimes timeout and trigger you to have to start again. Due to this concern, I decided to use targets to build a pipeline that could handle skipping downloads that were already successful if I needed to start again.

rOpenSci News Digest, July 2021

Fri, 23 Jul 2021 00:00:00 +0000

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

Great news for fans of statistics and software! rOpenSci’s peer-review system has now expanded to include review of packages implementing statistical routines and algorithms. We are thrilled to start this new chapter, for which we’ve developed a series of new standards and tools, and recruited a new board of experts to oversee. Authors of statistical software should begin by reading the Stats Software Dev Guide, which describes the categories of statistical software we now accept (Regression, Machine Learning, Exploratory Data Analysis, and more!), along with the procedures for preparing statistical software for peer review. It also introduces our automation tools, such as the pkgcheck package, which confirms that statistical software is ready to be submitted for review. Authors submitting statistical software to review should start by opening a pre-submission inquiry on our main software review repository. Inquiries are welcome well before packages are ready for submittal. We hope authors make use of our standards and tools throughout the development process so as to make review straightforward. To volunteer as a reviewer, fill our short form. For any question, you can post on the rOpenSci forum or contact the statistical software team (Mark Padgham, mark<at>ropensci.org, and Noam Ross, ross<at>ecohealthalliance.org).

pdftools + map to download & read multiple pdfs

Thu, 15 Jul 2021 00:00:00 +0000

rOpenSci package or resource used

other important packages: purrr and glue

What did you do?

I wrote code snippet that shows how to

create a list of URLs with glue::glue
download multiple pdfs using purrr::walk2
read them all with purrr::map & pdftools::pdf_text

URL or code snippet for your use case

Github code

Sector

academic / non-profit

Field(s) of application

humanities and any other field interested in downloading

pdftools + tesseract para extraer texto en español

Thu, 15 Jul 2021 00:00:00 +0000

rOpenSci package or resource used*

pdftools, tesseract

What did you do?

Convertí un texto-imagen en pdf a un texto legible para computadoras usando el OCR de Tesseract y la función de pdf_ocr_text()

URL or code snippet for your use case*

Código en Github

Sector

academic / non-profit

Field(s) of application

humanidades ¡y cualquier otra disciplina que use pdfs!

New package katex: rendering math to HTML and MathML in R

Tue, 13 Jul 2021 00:00:00 +0000

A new rOpenSci package katex is now on CRAN. This package allows for converting latex math expressions to HTML and MathML for use in markdown documents or package documentation.

The R package uses the katex javascript library, but the rendering is done directly in R using the V8 engine (i.e. server-side), which eliminates the need for embedding the MathJax library into html pages.

What it means to render server-side

To display a tex math in html we need a math typesetting library. The standard solution is to include MathJax with the html page, which attempts to convert math to html in the browser, upon loading of the webpage. However MathJax is quite heavy, which slows down the page, and it may not work in browsers where use of JavaScript or external libraries is restricted.

rOpenSci keynote, tutorial, talks, at useR!2021

Fri, 09 Jul 2021 20:00:00 +0000

Jeroen Ooms, rOpenSci Lead Infrastructure Engineer, will give a keynote talk about building a modern and scalable package build infrastructure, such as R-universe.

Maëlle Salmon, Research Software Engineer with rOpenSci, will give a tutorial, GET better at testing your R package! on Wednesday, July the 7th at 9-12AM GMT+2. This tutorial is about advanced testing of R packages, with HTTP testing as a case study.

Stefanie Butland, rOpenSci Community Manager, will present on rOpenSci’s Model for Managing a Federated Open Source Software Community.

Historical dataviz recreations with a sprinkle of magick

Sun, 04 Jul 2021 00:00:00 +0000

rOpenSci package or resource used*

What did you do?

As part of the #CottonViz challenge from the Royal Statistical Society, I used {magick} to:

create a gif that shows incrementally the steps I used to recreate Mary Eleanor Spear’s original data visualisation of US cotton supplies in the 1940s, made with manual methods
mimic another of Spear’s visualisations that uses ‘colour on the negative’, which she produced manually by ‘coloring negative photostat copies of charts or maps’

Functions used: image_read(), image_scale(), image_animate(), image_negate(), image_transparent(), image_background() and image_write().

Environment Canada air temperature using weathercan

Fri, 02 Jul 2021 00:00:00 +0000

rOpenSci package or resource used*

https://github.com/dosullivan019/30DayChartChallenge/blob/e4f5fe3e9d6245a5a65b7d617c785781eaaa5b69/code/day16_tree.R

Given the recent heatwave, I was curious about plotting up a timeseries of the local Environment Canada weather stations. For this, I used the weathercan package (https://github.com/ropensci/weathercan)

I’ll walk through the few lines of code that it takes to search, download, and plot the data:

First, load a couple libraries:

library(dplyr)
library(ggplot2)
library(weathercan)
library(ggrepel)

Then, search the station IDs that have data for this calendar year and match my city name.

rOpenSci at useR!2021 - Presentations from Staff and Community

Fri, 02 Jul 2021 00:00:00 +0000

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.

Stefanie Butland, Community Manager, will present on rOpenSci’s Model for Managing a Federated Open Source Software Community on Monday, July 5, 5:05PM UTC / 10:05AM PDT.

How We Curate Our Monthly Newsletter

Thu, 24 Jun 2021 00:00:00 +0000

How to keep up with rOpenSci? We agree that we’re doing so much good work that it’s hard. 😉 More seriously, we’ve been curating and sharing a news digest with our community for years because we believe it to be useful. Over time its structure and infrastructure have evolved. In this post we’ll share how we currently prepare content for the newsletter and send it to subscribers’ mailboxes, as automatically as possible.

Mapping Asian elephant observations with rgbif

Wed, 23 Jun 2021 00:00:00 +0000

rOpenSci package or resource used

rgbif

What did you do?

Searched GBIF for observations of Elephas maximus (Asian elephant), and used the locations for making two maps: one for the distribution as a heatmap, and one for observations themselves with a popup.

URL or code snippet for your use case

Code and Shiny web app

Image

Sector

Other

Field(s) of application

Ecology

How to create your personal CRAN-like repository on R-universe

Tue, 22 Jun 2021 00:00:00 +0000

R-universe: your personal R space

The r-universe platform provides users and organizations with a personal CRAN-like repository for publishing software, rmarkdown articles, and other content that fits in an R package.

The system automatically tracks registered git repositories containing R packages, builds binaries for Windows and MacOS, renders vignettes, and makes all data available through dashboards, feeds and APIs on personal subdomains, for example:

The initial pilot was mostly focused mainly on CRAN/rOpenSci developers, but as of last month we have opened up the system for anyone to create a personal R universe and start publishing packages.

rOpenSci News Digest, June 2021

Mon, 21 Jun 2021 00:00:00 +0000

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

You can read this post on our blog. Now let’s dive into the activity at and around rOpenSci!

rOpenSci HQ

R-universe

Video and resources from our past community call about rOpenSci’s R-universe Project were posted. The R-universe platform is a new umbrella project under which rOpenSci experiments with new ideas for improving publication and discovery of research software packages in R. In this 1-hour community call, Jeroen Ooms explained the basic steps of setting up your own universe, and getting started with publishing packages (including experimental software, development versions, research compendia) and articles on your personal subdomain.

Using rotl to create phylogenetic trees

Sat, 12 Jun 2021 00:00:00 +0000

rOpenSci package or resource used*

rotl

What did you do?

Used rotl to create a phylogenetic tree using a species scientific name and included clipart for each animal using phylopic.

URL or code snippet for your use case*

Image

Sector

other

Social Co-Working and Label-athon

Fri, 11 Jun 2021 01:30:00 +0000

We’re following up our Community Call - Set Up Your Package to Foster a Community - with an experiment!

Join us for 1.5 hours Thursday, June 10th, 5 PM Pacific / Friday June 11th 00:00 UTC for our fourth co-working “label-athon”.

Meet other package developers and rOpenSci staff in Zoom
Co-work independently, implementing some of our recommendations for what you can add/modify in your own package to encourage community participation
- Code of Conduct
- Contributing guide
- Roadmap and expectations
- Open and label issues to invite contributions
Get answers to your questions

At the end of the session we’ll tweet links to your “help wanted” issues to help you get attention to your project.

Celebrating World Ocean Day rOpenSci Style

Tue, 08 Jun 2021 00:00:00 +0000

Happy World Ocean Day!

World Ocean Day is a day of celebration and action to protect our shared ocean.

While I already appreciate the importance of protecting sensitive ecosystems, including the ocean¹, I found the idea of World Ocean Day especially touching.

On World Ocean Day, people around our blue planet celebrate and honor our one shared ocean, that connects us all.

About World Ocean Day

This year has been hard, and like many, I often feel isolated and emotionally exhausted. The idea that we have only one ocean and it connects us is a lovely way to remember that as isolated as we may feel we’re all here on this planet together.

Using tabulizer to extract tabular data from daily COVID-19 reports

Mon, 07 Jun 2021 00:00:00 +0000

rOpenSci package or resource used*

tabulizer

What did you do?

Used tabulizer to extract total cases, fatalities, hospitalizations, and tests from daily COVID-19 reports for Connecticut.

URL or code snippet for your use case*

https://github.com/davebraze/ct-covid19/blob/efc3afd6e86baf8ff7454f1d6a02d3e68feb6154/locals.R#L29

Sector

other

Social Co-Working and Label-athon

Thu, 27 May 2021 17:30:00 +0000

We’re following up our Community Call - Set Up Your Package to Foster a Community - with an experiment!

Join us for 1.5 hours Thursday, May 27th, 9 PM Pacific / 16:00 UTC for our third co-working “label-athon”.

Meet other package developers and rOpenSci staff in Zoom
Co-work independently, implementing some of our recommendations for what you can add/modify in your own package to encourage community participation
- Code of Conduct
- Contributing guide
- Roadmap and expectations
- Open and label issues to invite contributions
Get answers to your questions

At the end of the session we’ll tweet links to your “help wanted” issues to help you get attention to your project.

rOpenSci's R-universe Project

Tue, 06 Apr 2021 00:00:00 +0000

Index of video and slides

0:00 Stefanie Butland, Welcome and introductions
3:10 Jeroen Ooms, Getting started with R-universe
- 3:57 What is R-universe? (slides)
- 7:52 Browsing R packages in a universe (slides)
- 12:05 Browsing articles in a universe (slides)
- 14:07 API access to all the data! (slides)
- 17:00 For whom is R universe intended? (slides)
- 18:40 Example use-cases (slides)
- 28:48 Global feeds connect the universes (slides)
- 32:31 How to setup your own universe (slides)
41:07 Karthik Ram, Big picture and context for the R-universe project
42:58 Q & A

Setting up your own R universe

Earlier this year we announced R-universe: a project by rOpenSci under which we experiment with various ideas for improving publication and discovery of research software packages in R. The platform is under heavy development, Jeroen’s talk at rstudio-conf 2021 outlines some of our ambitions for the effort.

rOpenSci News Digest, May 2021

Fri, 21 May 2021 00:00:00 +0000

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

We have no less than three categories of (online 😉) events coming up: social co-working events, a community call, a conference with contributions from four rOpenSci staff members. ✨

Technical Debt in the Peer-Review Documentation of R Packages: a rOpenSci Case Study

Tue, 18 May 2021 04:00:00 +0000

rOpenSci Editor Melina Vidoni presents at MSR 2021 Mining Software Repositories Conference: Zadia Codabux, Melina Vidoni, Fatemeh Fard (2021). Technical Debt in the Peer-Review Documentation of R Packages: a rOpenSci Case Study. Preprint; Conference page.

Melina will present two additional talks:

Melina Vidoni (2021). Self-Admitted Technical Debt in R Packages: An Exploratory Study Preprint; Conference page. MSR 2021
Melina Vidoni (2020). Evaluating Unit Testing Practices in R Packages Preprint; Conference page. 43rd International Conference on Software Engineering ICSE 2021

Most tweeted words each month: a year snapshot

Mon, 17 May 2021 00:00:00 +0000

rOpenSci package or resource used

rtweet

Also used: gganimate, ggplot, lubridate. Code adapted from Julia Silge’s and David Robinson’s twitter case study in their book Text Mining with R and a helpful Stackoverflow answer by a user named Edward ;)

What did you do?

This was part of a final project for a course on Text Mining techniques. I analyzed the differences between three universities’ main Twitter accounts: @DukeU, @NCState, @UNC. I took a year snapshot of tweets utilizing rtweet and tried to find similarities and differences of what they were talking about. Covid19 was one of the key similarities, which makes sense given the year was dominated by the pandemic. You can see the progression of most frequently tweeted terms (tokenized by unigrams) by the use of gganimate + geom_text_wordcloud.

Social Co-Working and Label-athon

Fri, 14 May 2021 01:30:00 +0000

We’re following up our Community Call - Set Up Your Package to Foster a Community - with an experiment!

Join us for 1.5 hours Thursday, May 13th, 5 PM Pacific / Friday May 14th 00:00 UTC for our second co-working “label-athon”.

Meet other package developers and rOpenSci staff in Zoom
Co-work independently, implementing some of our recommendations for what you can add/modify in your own package to encourage community participation
- Code of Conduct
- Contributing guide
- Roadmap and expectations
- Open and label issues to invite contributions
Get answers to your questions

At the end of the session we’ll tweet links to your “help wanted” issues to help you get attention to your project.

Easily analyzing tweets using rtweet

Wed, 12 May 2021 00:00:00 +0000

rOpenSci package or resource used*

https://github.com/aarora79/30DayChartChallenge/tree/main/tweets

What did you do?

After the #30DayChartChallenge was over on April 30th, I wanted to make a summary of the twitter activity related to my tweets on the #30DayChartChallenge. All of the data for this analysis such as the tweets and user information were retrieved using rtweet, data wrangling done using tidyverse and visualization using ggplot2 and leaflet.

URL or code snippet for your use case*

Scraping Google Play Reviews with RSelenium

Tue, 11 May 2021 00:00:00 +0000

rOpenSci package or resource used*

RSelenium

What did you do?

Used RSelenium to scrape web reviews for Instagram Lite in order to do text analysis in a future blog post. The package was used to start a remote browser, browse to Google Play, and navigate the semi-infinite scroll and button clicks to load additional reviews.

URL or code snippet for your use case*

My Blog Post

Field(s) of application

Just for fun

What's New in terrainr 0.4.0?

Tue, 04 May 2021 00:00:00 +0000

terrainr version 0.4.0 is now on CRAN! This version is a relatively minor update that shouldn’t impact most workflows, but makes some changes to improve the logic and consistency of the package. The rest of this post runs through the changes you can expect if you update.packages any time soon!

What’s a terrainr?

terrainr is an R package for the retrieval and visualization of spatial data. It provides functions to download elevation data and basemap tiles for points within the United States (using public domain data from the USGS National Map), visualize them in R via ggplot2, and process them for 3D visualization using the Unity 3D engine. You can see the docs and access the GitHub repo here!

Social Label-athon

Thu, 29 Apr 2021 19:00:00 +0000

We’re following up our Community Call - Set Up Your Package to Foster a Community - with an experiment!

Join us for 1.5 hours Thursday, April 29, 9 AM Pacific / 16:00 UTC for our first co-working “label-athon”.

Meet other package developers and rOpenSci staff in Zoom
Work independently, implementing some of our recommendations for what you can add/modify in your own package to encourage community participation
- Code of Conduct
- Contributing guide
- Roadmap and expectations
- Open and label issues to invite contributions
Get answers to your questions

At the end of the session we’ll tweet links to your “help wanted” issues to help you get attention to your project.

Set Up Your Package to Foster a Community - Community Call Summary

Wed, 28 Apr 2021 00:00:00 +0000

Last Thursday we held a Community Call discussing how to set up a Package to Foster a Community.

This call included speakers Maëlle Salmon, Hugo Gruson and Steffi LaZerte, and was moderated by Stefanie Butland.

Summarizing the community call

Scientific software development - and with that R packages - is a community effort. While there are often just a handful of developers maintaining an R package, the development really starts to thrive when users start to contribute.

Set Up Your Package to Foster a Community

Wed, 24 Mar 2021 00:00:00 +0000

rOpenSci puts ongoing effort into exploring and communicating how developers can best attract attention to their package (e.g. usage, citations, or feedback), or how to set up their repository to encourage the types of contributions they want. In this 1-hour community call, Maëlle Salmon, Hugo Gruson, and Steffi LaZerte will share tips and examples on how to do this!

What is the community of a package or project?
Include a Code of Conduct
What goes in your package contributing guide? Etiquette and setup
Use your README to share your expectations with users and potential contributors
Use issue templates
Use issue labels to explicitly invite contributions (code or non-code) and user feedback
Include a roadmap so potential contributors know where your package is going, what you plan to implement, and what you won’t
What characteristics of a package or project make contributors keep coming back?

Come hear our best recommendations, and share your favorites. Stefanie Butland will moderate to get answers to your questions and we’ll have a collaborative notes doc to harness everyone’s collective wisdom.

rOpenSci News Digest, April 2021

Fri, 16 Apr 2021 00:00:00 +0000

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

Are you interested in volunteering as a package reviewer for rOpenSci? We have just updated our volunteering form to make it easier to match volunteers and packages. It only takes a few minutes to fill the form. Thanks to the more than 150 people who already answered, we’re very thankful for your participation!

Using RSelenium to scrape a paginated HTML table

Mon, 12 Apr 2021 00:00:00 +0000

rOpenSci package or resource used*

RSelenium

What did you do?

This example explains how emulate clicks can be done to navigate from elements to others in the HTML page, and a more focus point on moving from page to page in a paginated table.

URL or code snippet for your use case*

Blog post here

Publishing and browsing articles on R-universe

Fri, 09 Apr 2021 00:00:00 +0000

Browsing articles on R-universe

In the past weeks we have extended the R-universe build system and front-ends with some new features for publishing articles. Articles can be used for documentation of R packages, but also for other purposes, such as reports, tutorials, papers, or research compendia. Publishing of articles in R-universe is based on the R vignette system, and we may add support for other types of articles later on.

Maëlle Salmon Teaches R-pkg Dev at R-Ladies East Lansing & Chicago

Fri, 26 Mar 2021 19:00:00 +0000

“Develop an R package”, they said… What does this even mean?

In this session with a live demo, we shall demystify the creation of an R package. R packages are mostly well-organized folders, and there are automatic tools to help. Let’s dive into the wonders of usethis! We shall also see why to create a package (or not). We shall furthermore explain how to improve your R package and your own package development skills. And how to solve the specific new challenges you will encounter! Last but not least we will discuss how to find your happy place in the world of R package development.

Teaching an introduction to workflow management using drake

Thu, 25 Mar 2021 00:00:00 +0000

rOpenSci package or resource used*

drake

What did you do?

In fall 2020 the Center for Environmental Research, Education and Outreach at Washington State University hosted a workshop covering reproducible research techniques in R for graduate students. We wanted to cover drake workflows as one day of the workshop to show the students what R-specific options there are for managing workflows. We expected that workflow management and to some extent R functions would be unfamiliar topics to many students, so the workshop day included discussion of why one would use workflow management software and some basic examples of building realistic functions. At the time that we ran the workshop I wasn’t aware of targets, so in the future we may repurpose this example using that package instead.

Latest rOpenSci News Digest

Tue, 16 Mar 2021 00:00:00 +0000

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 page on our website! 🚀 The R-universe platform is a new umbrella project under which we experiment with various new ideas for improving publication and discovery of research software in R.

rOpenSci Statistical Software Testing and Peer Review - Community Call Summary

Tue, 09 Mar 2021 00:00:00 +0000

A week ago we held a Community Call discussing rOpenSci Statistical Software Testing and Peer Review. This call included speakers Noam Ross, Mark Padgham, Anna Krystalli, Alex Hayes, and John Sakaluk.

This post provides a ready reference and description of this community call, which introduced the system being developed for peer review of explicitly statistical software, along with a couple of the automated software tools for use by developers and reviewers of statistical software.

A first look at the R-universe build infrastructure

Thu, 04 Mar 2021 00:00:00 +0000

The R-universe build system

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

A lot of the early work on R-universe has gone into iterating with designs to gradually build up such a system in a way that is robust and scalable, while keeping complexity under control.

rOpenSci Statistical Software Testing and Peer Review

Wed, 17 Feb 2021 00:00:00 +0000

This is the first in a series of Community Calls we’ll host throughout the year on our statistical software review project.

We at rOpenSci are in the process of expanding the scope of our software peer-review system to encompass explicitly statistical software. As part of this we have developed new tools to help prepare software for submission. One of these, the autotest package, implements and automates rigorous testing of all function inputs, while another, the srr package, enables documentation of, and reporting on, how and where code meets our sets of category-specific standards. Developers of packages to be submitted to this newly expanded system will be expected to apply both of these tools prior to submission.

Using terrainr to retrieve spatial data and make 3D landscape visualizations

Mon, 01 Mar 2021 00:00:00 +0000

rOpenSci package or resource used*

terrainr

What did you do?

Visualized Mt. St. Helens in Unity, using public-domain data from the USGS entirely retrieved and pre-processed in R.

URL or code snippet for your use case*

library(terrainr)
library(sf)
library(progressr)
handlers("progress")
st_helens <- data.frame(
lat = 46.1914,
lng = -122.1956
)
st_helens <- st_as_sf(st_helens, coords = c("lng", "lat"))
st_helens <- st_set_crs(st_helens, 4326)
st_helens <- set_bbox_side_length(st_helens, 8000)
with_progress(
output_tiles <- get_tiles(st_helens,
services = c("elevation", "ortho"))
)
merged_tiles <- vapply(output_tiles, merge_rasters, character(1))
mapply(
function(x, y) raster_to_raw_tiles(x, "st_helens", raw = y),
merged_tiles,
c(TRUE, FALSE)
)

This gets you a set of files in the format that Unity expects. You still need to import them by hand (for now…) – see the Unity vignette for more on that!

rOpenSci Dev Guide 0.6.0: Updates

Tue, 23 Feb 2021 00:00:00 +0000

rOpenSci Software Peer Review’s guidance is gathered in an online book and keeps improving! To find out what’s new in our dev guide 0.6.0, you can read the changelog, or this blog post for more digested information.

We have resumed activity after a break due to the COVID-19 crisis, but are being gentle with deadlines and timing, giving a lot of grace to all people involved. We’re all doing our best and rOpenSci is trying to be accommodating with schedules during this challenging period.

Make Your R Package Easier to Cite

Tue, 16 Feb 2021 00:00:00 +0000

Scientists rarely cite research software they use as part of a research project. As a consequence, the software and the time spent developing and maintaining it becomes an invisible scholarly contribution. Furthermore, this lack of visibility means that incentives to produce high quality, sustainable software are missing. Among many reasons why software is not cited, one is the lack of a clear citation information from package developers. In this tech note we provide some tips on how to make it really easy to cite your software.

coder Makes Medical Coding less Messy

Tue, 09 Feb 2021 00:00:00 +0000

A new R-package, coder, has been developed, peer-reviewed by rOpenSci, accepted by CRAN, and published in a paper by the Journal of Open Source Software (JOSS). In this blog post, I will explain why this package might be useful for (epidemiological/medical/health care related) research.

Clinical mess

Once upon a time, in countries not far from ours, there were MDs and nurses making up funny names for any diseases they encountered. What Dr. A called X would be recognized only as Y by his dear colleague Dr. B. X, however, was also a name used by Dr. C, but then for a completely different condition. It was a mess!

Mapping collaborations in Neotropical Taxonomy with refsplitr

Sat, 06 Feb 2021 00:00:00 +0000

rOpenSci package or resource used*

refsplitr

What did you do?

To demonstrate the importance of taxonomy for the study of Neotropical biodiversity, the authors (1) showcase selected plant groups in which in-depth taxonomic understanding has facilitated evolutionary and ecological research and (2) map the teams of collaborating scientists.

URL or code snippet for your use case*

https://doi.org/10.3417/2020601

Image

Sector

Academic

Field(s) of application

Botany, Ecology, Tropical Biology, Bibliometrics, Science of Science

targets: Democratizing Reproducible Analysis Pipelines

Wed, 03 Feb 2021 00:00:00 +0000

Make¹-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.

…looking to get your project/s organised in the new year? hoping just to distract from feelings of impending doom/crushing loss of hope? I promise workflowing will make you feel better… and @wmlandau has made it SO EASY.

How rOpenSci Runs Community Calls

Tue, 02 Feb 2021 00:00:00 +0000

rOpenSci community calls are online events with the fundamental goal of strengthening our community. We have the additional goals of reinforcing our mission and values, informing people on technical and social topics, bringing different stakeholders’ perspectives to light, and identifying unmet needs on a topic. Calls can include one to six speakers, or a moderated panel discussion. They run for an hour and consist of 40 minutes of presentation and 20 minutes for questions from the audience. Generally, our calls attract fairly large audiences¹ and we see significant representation from academia, government, and industry.

Use gert to scan all git repos in a directory

Mon, 01 Feb 2021 00:00:00 +0000

rOpenSci package or resource used*

gert

What did you do?

wrote a function that scans a directory looking for git repositories that may need to be pushed to (or pulled from) github
this example is based on the git_ahead_behind() command but it could easily generalise to other kinds of checks

URL or code snippet

github gist

Behind the magick: updates to imagemagick and beyond

Fri, 29 Jan 2021 00:00:00 +0000

It has been a while since we posted an update about magick, but behind the scenes we are constantly tweaking and improving this package, which has become a very mature and complete toolkit for image processing in R.

Over the past year, we did 6 CRAN releases, containing many small features and fixes, but perhaps more importantly, the package is getting betting better due to updates of the underlying ImageMagick library.

As mentioned in the NEWS, magick 2.6.0 gains support for “raw” and “heif” delegates on Windows and MacOS. The raw delegate is based on libraw which allows reading RAW files obtained from digital photo cameras. Heif is a new library that provides a set of formats for high quality (Ultra HD+) images in HEVC and AV1 format. Support for these formats was requested by users of the R magick package.

Learn All About HTTP Testing: Book Update

Tue, 26 Jan 2021 00:00:00 +0000

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 secrets, etc. Having tests fail due to resources being down or slow, during development or on CRAN, means a time loss for everyone involved (slower development, messages from CRAN). Although many packages accessing remote resources are well tested, there used to be a lack of resources around best practices… But now there is one great information source, our HTTP testing in R online book! 🎉

pdftools for extracting complex (e.g. text-wrapped/multiline) tables from pdfs

Tue, 26 Jan 2021 00:00:00 +0000

Extracting a complex table from pdf using pdftools::pdf_data. Example uses a table spread over multiple pages, and containing multiple(text-wrapped) lines per cell, and left and centre justified cell entries.

rOpenSci package or resource used*

What did you do?

Extraction of complex tables from a pdf document, based on data extracted by pdftools::pdf_data(). Example has a table spread over multiple pages, and text wrapping across multiple lines per cell.

Shiny apps to search #rstudioglobal or #rstats tweets with rtweet

Mon, 25 Jan 2021 00:00:00 +0000

rOpenSci package or resource used*

Created interactive app and tutorials

I created an interactive Shiny apps for people to easily search, sort, filter, and download tweets with the #rstudioglobal or #rstats hashtags. #rstudioglobal was for the RStudio Global 2021 conference; #rstats is for any R tweet tagged with that hashtag. I also created two tutorials for others who would like to do something similar.

URL or code snippet for your use case*

rstats app: http://apps.machlis.com/shiny/rstats rstudioglobal app: http://apps.machlis.com/shiny/rstudioglobal/ Basic rtweet tutorial at InfoWorld: https://www.infoworld.com/article/3515712/how-to-search-twitter-with-rtweet-and-r.html Bonus tutorial on turning rtweet data into a Shiny app: https://www.infoworld.com/article/3516150/create-a-shiny-app-to-search-twitter-with-rtweet-and-r.html

Using dittodb to test database queries

Mon, 25 Jan 2021 00:00:00 +0000

rOpenSci package or resource used*

dittodb

What did you do?

I have a few functions in an internal package which basically wrap up some database queries. These are tricky to test because my CI system is not allowed to connect directly to the databases. dittodb let’s me do two things with these functions:

Test them in an automated way
Have a record of what the ‘correct’ database response looked like in case the data source changes down the road

URL or code snippet for your use case*

getData <- function(date) {
cred <- .getMyCredentials("mydb")
con <- DBI::dbConnect(
RPostgreSQL::PostgreSQL(),
user = cred["user"],
password = cred["password"],
dbname = cred["dbname"],
host = cred["host"],
port = cred["port"]
)
on.exit(DBI::dbDisconnect(con))
out <- tbl(con, "my_table") %>%
dplyr::filter(.data$date > local(date))
return(out)
}
dittodb::with_mock_db({
test_that("getData", {
results <- getData("2010-01-01")
expect_s3_class(results, "data.frame")
expect_named(results, c("date", "value", "state"))
})
})

Chat with rOpenSci team members at rstudio::global

Fri, 22 Jan 2021 16:00:00 +0000

rOpenSci is proud to be a Community Partner at rstudio::global 2021 January 21-22, 2021.

Come chat with members of our team about developing high-quality R-packages for research, best practices in software peer review, the R-universe project, or building community. Ask us anything.

You can find us in the conference’s Spatial.Chat Community Partners Room at the rOpenSci table.

Jan 21st 9:20am PST; 12:20pm EST; 6:20pm CET
Jan 21st 1:20pm PST; 4:20pm EST; 10:20pm CET
Jan 21st 5:20pm PST; 8:20pm EST; 2:20am CET
Jan 22nd 1:20am PST; 4:20am EST; 10:20am CET
Jan 22nd 5:20am PST; 8:20am EST; 2:20pm CET

Look for some of our community neighbors who will be there too, like MetaDocencia, Openscapes, The Carpentries, and others.

Monitoring health and impact of open-source projects

Thu, 21 Jan 2021 23:20:00 +0000

Jeroen Ooms talked about his rOpenSci work at rstudio::global 2021

Abstract

At rOpenSci, we have come to realize that in order to help researchers get the most out of R, we need better tooling to monitor the quality, health, and impact of R packages. This applies both to our internal projects, as well as other packages in the R ecosystem. But what exactly makes a good R package?

In this talk we discuss various aspects of open-source software that are not always immediately obvious, and that you may want to consider when depending on an R package. We identify several categories of indicators you could look for, ranging from the role in the dependency network, to expectations around maintenance and participation.

Getting and plotting weather and climate data

Thu, 21 Jan 2021 00:00:00 +0000

rOpenSci package or resource used*

What did you do?

I took my undergrad limnology class on a field trip to sample & characterize a local storm water retention pond in Brandon MB. Both weather and climate can provide important context when interpreting results. I used Steffi’s weathercan package to get Environment and Climate Change Canada weather & climate data for Brandon MB. I plotted up this data a few different ways and as a class we discussed how to best present this data.

Introducing the rOpenSci Community Contributing Guide

Wed, 20 Jan 2021 00:00:00 +0000

Many people in our community actively contribute to rOpenSci projects. Many others would like to contribute but aren’t sure how to go about it. Wanting to get involved in rOpenSci or “give back to open source” means different things to different people. Ideally, a person should be able to find a way to contribute that meets their needs and fits our mission. We created the rOpenSci Community Contributing Guide¹ to make finding paths to contributing more transparent and sustainable.

Introducing BaseSet for mathematical sets

Tue, 19 Jan 2021 00:00:00 +0000

In this post I will explain the history behind BaseSet then a brief introduction to sets, followed by showing what you can do with BaseSet.

Brief BaseSet history

I study diseases to try to find what causes them at a research institute associated with an hospital. Thanks to recent technological advances we can analyze many things from a single patient’s sample. Having so much information available can be overwhelming, making it difficult to find the causes of diseases (but it is much better than not having enough information!).

Using ghql to analyze all my 2020 GitHub commits

Sat, 16 Jan 2021 00:00:00 +0000

rOpenSci package or resource used

ghql

What did you do?

I had a Twitter bot summarize my 2020 contributions on GitHub. I was a bit surprised by the high number of commits that I had made so I decided to have a look into that. I used the GitHub GraphQL API via the ghql package to first pull all the repositories I had contributed to in the past and in a second step get all my commits to those repositories. I then had a look at the “smaller commits” to check whether “~30% of my commits were 1 line diffs” which was my main hypothesis for the high number of commits (spoiler: no, only ~12%). I also had a look at the files that I changed in those small commits (using the REST API via gh). In theory and with some tweaks (mostly adding pagination to the first step), the data collection approach via ghql should be able to give you all your commits to the default branch over all repositories you have committed to. 🤯

rOpenSci 2020 Code of Conduct Transparency Report

Thu, 07 Jan 2021 00:00:00 +0000

rOpenSci Code of Conduct Annual Review

Thu, 07 Jan 2021 00:00:00 +0000

Scraping liked posts on Twitter using rtweet

Sun, 03 Jan 2021 00:00:00 +0000

rOpenSci package or resource used*

https://ivelasq.rbind.io/blog/get-tweet-likes/

What did you do?

I used rtweet to recreate a Python tutorial on scraping your liked Tweets on Twitter using R.

URL or code snippet for your use case*

Field(s) of application

For fun (and being able to more easily scroll through your liked Tweets)

Phonetic Fieldwork and Experiments with the phonfieldwork Package for R

Tue, 22 Dec 2020 00:00:00 +0000

Science craft

As a field linguist, I have spent a lot of time working in villages in the Caucasus, collecting audio from speakers of indigenous languages. The processing of such data involves a lot of time-consuming tasks, so during my field trips I created my own pipeline for data collection. I wrote a number of scripts using different programming languages for automatic renaming, merging, and preannotation of files, making backups, visualizing some data, etc. My method consisted of a combination of solutions developed on the fly to solve specific, independent tasks, without thinking of the future.

2 Months in 2 Minutes - rOpenSci News, December 2020

Fri, 18 Dec 2020 00:00:00 +0000

rOpenSci HQ

We’re thrilled to announce three new rOpenSci Software Review Editors: Laura DeCicco, Julia Gustavsen, and Mauro Lepore and we released the fifth version (v0.5) of the rOpenSci Developer Guide.

Our Community Call on The Wild World of Data Repositories took place Dec 16 with an audience of 153 people! The video will be posted, along with collaborative notes and resources, by Dec 21.

Software Peer Review

2 community-contributed packages passed software peer review.

HTTP Testing With the Newest Release of vcr

Fri, 18 Dec 2020 00:00:00 +0000

A new version of vcr was just released. See the release notes for all the details. I want to highlight a few of the more notable changes.

New contributor

vcr has a new author: Maëlle Salmon. She has been contributing to the package quite a lot lately, including many documentation improvements and big updates to the HTTP Testing in R which covers vcr in addition to some other packages.

New serializer

vcr now has two serializer options: YAML (which we had before) and JSON (the new one). Serializing here refers to what format the HTTP request and response are put in before being written to a file. If you’re a keen observer of these two data formats, you’ll know these are not that different, with YAML a superset of JSON. The clear advantage of JSON straight away is that it avoids the common problem with vcr enabled tests on Windows platform where using YAML leads to errors due to something about the yaml package. The jsonlite package, which does the heavy lifting when using JSON, does not suffer from the same problems on Windows.

The Wild World of Data Repositories

Wed, 18 Nov 2020 00:00:00 +0000

See below for speaker bios and resources including collaborative notes from the call.

There is no one-size-fits-all protocol for depositing your research data into a public repository in a way that maximizes its reuse and citation. We’ve assembled a panel that will help you understand the issues and opportunities for developing new tools and documentation.

This 1-hour event, moderated by Kara Woo, includes 5 speakers and 20 minutes for Q & A on:

Donate to rOpenSci this Giving Season

Wed, 16 Dec 2020 00:00:00 +0000

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. Our community in collaboration with our staff produce and maintain a vast collection of free open source software to support and accelerate scientific discovery. Hundreds of people have contributed their creativity, curiosity, smarts, and time in the last year. For a glimpse, see Thank You to the rOpenSci Community, 2020.

Thank You to the rOpenSci Community, 2020

Tue, 15 Dec 2020 00:00:00 +0000

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.

On behalf of rOpenSci, thank you.

Using av to convert audio files for compatibility with an electronic storyteller

Thu, 10 Dec 2020 00:00:00 +0000

rOpenSci package or resource used*

What did you do?

I converted tracks of stories for compatibility with my kids’ electronic storyteller with R instead of having to use the manufacturer’s online web interface.

URL or code snippet for your use case*

https://masalmon.eu/2020/12/10/av-storytime/

Sector

other

Field(s) of application

little kids wrangling 😁

Accessing GraphQL from R

Tue, 08 Dec 2020 00:00:00 +0000

Introduction

Few months ago, I embarked on a full stack spatial data project at work. The project kicked off amazingly, until I was almost backed to the wall when I discovered that some of the data sources were served via a GraphQL API. Before now, I haven’t worked with GraphQL. But, I have heard a lot about it and how amazing it is for querying data.

GraphQL is a query language for application programming interfaces (APIs) that prioritizes giving clients exactly the data they request. It’s designed to make APIs flexible, fast and friendly. Basically, it is used to load data from a server to a client and it does this in a much more efficient manner than traditional methods and services.

Selecting the Best Phylogenetic Evolutionary Model

Tue, 01 Dec 2020 00:00:00 +0000

With this blog post, I show how to use the mcbette R package in an informal way. A more formal introduction on mcbette can be found in the Journal of Open Source Science ¹. After introducing a concrete problem, I will show how mcbette can be used to solve it.

After discussing mcbette, I will conclude with why I think rOpenSci is important and how enjoyable my experiences have been so far.

Handling vegetation-plot information using vegtable and taxlist

Sat, 21 Nov 2020 00:00:00 +0000

rOpenSci package or resource used*

taxlist

What did you do?

Brief explanation about the use of the packages taxlist and vegtable, the second embedding the first. Functions used to produce descriptive statistics and especially to calculate proportions of higher level taxonomic ranks in plot observations and to count taxa are also briefly introduced.

URL or code snippet for your use case*

https://kamapu.github.io/posts/2020-11-20-vegtablepress2/

Image

Sector

academic

Moving away from Travis CI

Thu, 19 Nov 2020 00:00:00 +0000

At rOpenSci, we encourage R package developers to take advantage of Continuous Integration services to automatically check the package on different platforms, with different versions of R. The rOpenSci dev guide dedicates chapter 2 to the topic of Continuous Integration Best Practices, and recommends a few common CI vendors, including Travis CI.

Travis CI has been a pioneer in free public CI services, and made the concept popular in the open-source community. The service started to get wide adoption in 2012, and native support for R was added by Craig Citro in 2015, with more contributions from current maintainers Jim Hester and later Jeroen. In 2016 we wrote a blog post about using a build-matrix in order to check your packages on multiple versions of Linux and MacOS, which is super powerful for R package development.

Use stplanr to find and plot major streets of a city

Wed, 18 Nov 2020 00:00:00 +0000

rOpenSci package or resource used*

stplanr package

What did you do?

The life lines of Berlin

A fast way to find major streets within a city, without searching for any data on traffic amounts, street types or street width:

Take random start and end points within the city and run a routing to find routes connecting the start and end points.

Then aggregate the single street segments on how often they were used. You then get an image of the major city axes.

fulltext: Behind the Scenes

Tue, 17 Nov 2020 00:00:00 +0000

fulltext is a package I maintain for text-mining the scholarly literature (package docs). You can search for articles, fetch article metadata and abstracts, and fetch full text of some articles. Text-mining the scholarly literature is a research tool used across disciplines. Full text of articles (entire article, not just the abstract) is the gold standard in text-mining in most cases.

Over the past years the fulltext package has evolved under the hood in its approach to attempting to get full text articles for its users. The following is a walk through of the various iterations that fulltext has gone through for fetching full text of articles. I think it serves as a good demonstration of the complexity and frustration baked into the publishing industry, as well as the trade-offs of various approaches to solving problems and getting things done.

Installing V8 is now even easier

Thu, 12 Nov 2020 00:00:00 +0000

Google’s amazing V8 JavaScript/WASM engine is probably one of the most sophisticated open-source software libraries available today. It is used to power the computation in Google Chrome, NodeJS, and also CloudFlare Workers, which make it possible to run code for your website inside the CDN edges.

The R package V8 exposes this same engine in R, and has been on CRAN since 2014. It is used by many R packages to wrap JavaScript libraries, such as geojsonio, jsonld, DiagrammeR, or almanac. Recently we have seen an increase in usage because the latest version of rstan now uses V8 for their parser.

Navigating open-source software: Ensuring you can rely on what you use

Wed, 11 Nov 2020 11:00:00 +0000

Dr Rebecca Killick, Associate Professor in the Mathematics & Statistics department at Lancaster University, and member of rOpenSci’s Statistical Software Peer Review committee spoke at the National Health Service R (NHS-R) Community annual meeting. The audience included everyone from Clinicians to data managers.

Using Open-Access Tools (rentrez, taxize) to Find Coronaviruses, Their Genetic Sequences, and Their Hosts

Tue, 10 Nov 2020 00:00:00 +0000

Emerging viruses might be on everyone’s mind right now, but as an epidemiologist and disease ecologist I’ve always been interested in how and why pathogens move from animal hosts to humans. The current pandemic of the disease we call COVID-19 is caused by Severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2), a virus that has emerged from wildlife like SARS coronavirus and Middle East respiratory syndrome (MERS) coronavirus did previously. Although these viruses are now widely known, there are many more coronaviruses out there in nature, many of which we know little about.

osmdata, rnaturalearth and magick for #TidyTuesday

Fri, 06 Nov 2020 00:00:00 +0000

rOpenSci package or resource used*

osmdata, rnaturalearth, magick

What did you do?

I used these packages to create my submission for week 44 of #TidyTuesday, Canadian Wind Turbines. TidyTuesday is a weekly social visualization activity/project/challenge originating out of the R4DS and larger R community. rnaturalearth provided me with an excellent map of Maritime Canada, osmdata for the main highways (using simple features too!) and magick for the no-fuss image cropping!

Announcing New Software Peer Review Editors: Laura DeCicco, Julia Gustavsen, Mauro Lepore

Tue, 27 Oct 2020 00:00:00 +0000

We are pleased to welcome Laura DeCicco, Julia Gustavsen, and Mauro Lepore to our team of Associate Editors for rOpenSci Software Peer Review. They join Brooke Anderson, Anna Krystalli, Karthik Ram, Noam Ross, Maëlle Salmon, and Melina Vidoni. Lincoln Mullen and Scott Chamberlain are now board alumni.

Since 2015, rOpenSci has been running a software peer review system to combine the best of academic peer review with software review. Having robust and reliable software tools is an important component of supporting open science and reproducible research. Editors manage the review process, performing initial package checks, identifying reviewers, and moderating the process until the package is accepted by reviewers and transferred to rOpenSci.

osmdata: Rail transport network of the three largest cities in Spain

Tue, 27 Oct 2020 00:00:00 +0000

rOpenSci package or resource used*

osmdata

What did you do?

I combined several functions from the osmdata package to download the vector data for the street grid and rail transport network of the three largest cities in Spain (Madrid, Barcelona and València) and try to produce a nice-looking plot of these cities.

URL or code snippet for your use case*

https://github.com/GuillemSalazar/r_miscellanea/blob/72a477161e6fd5dfaad9661665cc9f38fa73060e/doc/1_osm.md

Image

R-Ladies East Lansing Meetup

Thu, 22 Oct 2020 21:00:00 +0000

Stefanie Butland, rOpenSci’s Community Manager, will introduce rOpenSci and our new Contributing Guide.

Brooke Anderson, an rOpenSci Software Peer Review Editor (and Assistant Professor of Epidemiology and a Faculty Associate in the Department of Statistics at Colorado State University in her day job) will introduce people to our peer review process.

R-Ladies East Lansing’s information on who can attend: “We encourage women and minority genders to present/lead most sessions, conversations but we have no restrictions whatsoever when it comes to membership, participation, and discussions. So, please join us and bring your R-family & R-friends!” More information on their Meetup page.

rOpenSci Dev Guide 0.5.0: Updates

Thu, 22 Oct 2020 00:00:00 +0000

rOpenSci Software Peer Review’s guidance has been compiled in an online book for more than one year now. We’ve just released its fifth version. To find out what’s new in our dev guide 0.5.0, you can read the changelog, or this blog post for more digested information.

We have resumed activity after a break due to the COVID-19 crisis, but are being gentle with deadlines and timing, giving a lot of grace to all people involved. We’re all doing our best and rOpenSci is trying to be accommodating with schedules during this challenging year.

Searching medRxiv and bioRxiv Preprint Data

Tue, 20 Oct 2020 00:00:00 +0000

Background & motivation

medRxiv, as the preprint repository for papers in the medical, clinical, and related health sciences,¹ has become a central source of new studies related to the COVID-19 pandemic. As a result, more and more researchers have begun to include medRxiv in the list of bibliographic databases they search as part of systematic reviews, a type of study that aims to find and bring together all available evidence on a topic in order to provide a comprehensive answer to a research question.

2 Months in 2 Minutes - rOpenSci News, October 2020

Thu, 15 Oct 2020 00:00:00 +0000

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.

Contributing Guide Release

The purpose of our new Contributing Guide is to welcome you to rOpenSci and help you recognize yourself as a potential contributor. It will help you figure out what you might gain by giving your time, expertise, and experience; match your needs with things that will help rOpenSci’s mission; and connect you with resources to help you along the way.

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

Tue, 13 Oct 2020 00:00:00 +0000

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. The looming spectre of a second wave of the pandemic has spurred around-the-clock research efforts to better understand the pathology and epidemiology of the virus, in the hope of new therapies and vaccines. And while novel scientific information about the pandemic was being shared at an unprecedented rate in the form of preprints¹, it was becoming difficult to get an accurate, trustworthy record of this information.

ReproHack en LatinR

Thu, 08 Oct 2020 20:00:00 +0000

Miguel Alvarez (author of rOpenSci peer-reviewed package taxlist) and Maëlle Salmon (associate editor) will both record a short talk presenting rOpenSci Software Peer Review to be shown during “ReproHack en LatinR”. Anna Krystalli (associate editor, ReproHack creator) will answer questions.

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

Tue, 06 Oct 2020 00:00:00 +0000

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 wanted issues in rOpenSci packages, it provides suggestions on etiquette to maximize the chances that your effort will be appreciated by a maintainer.

Rectifying Hand-Drawn Marks on Maps With the mapscanner Package

Tue, 29 Sep 2020 00:00:00 +0000

mapscanner

It is sometimes easy in the midst of the cutting-edge world of unique software development that is rOpenSci to forget that even though our software might be freely available from anywhere in the world, access to adequate hardware is often restricted. Restricted access to hardware is rarely acknowledged as a reason for differing outcomes from the practice of science in different parts of the world, yet being in a part of the world that is relatively less financially advantaged must translate to being relatively less able to take advantage of the abilities of computer hardware.

A Twitter bot with rtweet, Mapbox and GitHub Actions

Fri, 25 Sep 2020 00:00:00 +0000

rOpenSci package or resource used*

https://conbio.onlinelibrary.wiley.com/doi/10.1111/csp2.270

What did you do?

I set up a GitHub Action that includes R code that generates random coordinates in greater London, queries the Mapbox API for a satellite image and uses the Twitter API via {rtweet} to post the image to the @londonmapbot Twitter account.

URL or code snippet for your use case*

Image

The treedata.table Package

Tue, 22 Sep 2020 00:00:00 +0000

The data.table package enables high-performance extended functionality for data tables in R. treedata.table is a wrapper for 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 in base R, enabling processing of larger trees and datasets.

Why use treedata.table?

Simultaneous processing of phylogenetic trees and data remains a computationally-intensive task. For example, processing a tree alongside a dataset of phylogenetic characters means processing much more data compared to processing the characters alone. This results in much longer processing times compared to more simple analysis with characters alone in data.table (Fig. 1A). treedata.table provides new tools for increasing the speed and efficiency of phylogenetic data processing. Data manipulation in treedata.table is significantly faster than in other commonly used packages such as base (>35%), treeplyr (>60%), and dplyr (>90%). Additionally, treedata.table is >400% faster than treeplyr during the initial data/tree matching step (Fig. 1B).

Kontarion - a stack extending rocker/ml-verse for Bibliometric analytics

Tue, 15 Sep 2020 00:00:00 +0000

The larger use case for Kontarion is to support developing and deploying Bibliometric analytics within the KTH Royal Institute of Technology Library - a container-based platform that can be used on-prem or in the cloud.

rOpenSci package or resource used

oai, rentrez, fulltext, europepmc, refsplitr, rcrossref, citecorp, roadoi

What did you do?

Assembled a stack extending the versioned rocker-project.org docker image for ml-verse with various ROpenSci (and other) packages, to provide a containerized platform supporting Bibliometric analysis workflows.

Mapping scientific collaboration about the Anthropoce with refsplitr

Tue, 15 Sep 2020 00:00:00 +0000

rOpenSci package or resource used*

Package refsplitr

What did you do?

The authors studied the location and patterns of collaboration of authors publishing research on the Anthropocene.

URL or code snippet for your use case*

Image

Sector

academic

Field(s) of application

academic publishing, conservation biology, text analysis, scientometrics, bibliometrics, science of science

Processing Web of Science records with refsplitr to study author gender and geography

Tue, 15 Sep 2020 00:00:00 +0000

rOpenSci package or resource used*

Package refsplitr

What did you do?

The authors examined how author location, author gender ratios, and publication rates in myrmecology changed over three decades.

URL or code snippet for your use case*

https://myrmecologicalnews.org/cms/index.php?option=com_content&view=category&id=1568&Itemid=435

Image

Sector

academic

Field(s) of application

academic publishing, myrmecology,gender diversity, scientometrics, bibliometrics, science of science

covidpreprints.com using europepmc and rAltmetric

Tue, 08 Sep 2020 00:00:00 +0000

rOpenSci package or resource used*

europepmc, rAltmetric

What did you do?

covidpreprints.com is a one-stop portal for the lay public and scientific community. We created covidpreprints.com to promote scientific education and combat misinformation by discussing controversial scientific issues. We focus on the trend of open access in science, especially in the form of preprints, and we see it as a way to shape the growth of these trends within the scientific community.

Scientific Name Parsing: rgnparser and namext

Tue, 25 Aug 2020 00:00:00 +0000

I’m starting to tackle a few hard packages (spplit and spenv) having to do with integrating disparate data sources. I’ll talk here about spplit. I haven’t worked on spplit in a few years; I thought I’d make another attempt with “fresh” eyes.

There are many use cases I can imagine for spplit; I’ll highlight a few. First, one may want to find literature that mentions particular scientific names (find all the journal articles that include the name Ursus americanus (American black bear)). Second, one could extract scientific names from scientific literature to examine the different formats of scientific names used in different journals (e.g., Homo sapiens vs. Homo sapiens Linnaeus vs. Homo sapiens Linnaeus, 1758). Last, you could extract the scientific names from your own manuscript before submission to check that all scientific names are properly formatted and match your preferred taxonomic reference.

Bar chart portraits with magick

Sun, 23 Aug 2020 00:00:00 +0000

rOpenSci package or resource used*

Code: https://github.com/gkaramanis/aRt/tree/master/split-bar

What did you do?

I used magick to resize and convert an image to grayscale, and then to get the pixel values that represent their brightness. The values were used to make horizontal bars at the position of each pixel, with the width of the bar corresponding to reverse brightness (longer bars = brighter pixels).

URL or code snippet for your use case*

2 Months in 2 Minutes - rOpenSci News, August 2020

Thu, 20 Aug 2020 00:00:00 +0000

rOpenSci HQ

Join our Community Manager Stefanie Butland in a CarpentryCon @ Home fireside chat on Growing Inclusive, Computational Communities and Leaders. Live 90-min discussions Wed Aug 26 21h00 (2pm PDT) and Thu Aug 27 15h00 UTC (8am PDT). Other panelists over the two sessions are Abigail Cabunoc Mayes (Mozilla Foundation), Kate Hertweck (Fred Hutch Cancer Research Center), Toby Hodges (The Carpentries), Angela Li (U Chicago), Marlene Mhangami (Python Software Foundation), Naomi Penfold (eLife), and Serah Rono (The Carpentries). Submit your questions for the panel before Aug 24.

Developing dittodb

Tue, 18 Aug 2020 00:00:00 +0000

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.

The idea

The idea for dittodb came as a very practical one: at my day job I was working on an R package that interacted with our databases. Though we could test a lot of things, we were struggling with writing good tests for our database interactions. We could technically connect to the actual production database, but that meant that the tests were slow and depended on data that was sometimes changing¹. Worst of all: it would mean having to store our database credentials in our Continuous Integration infrastructure.

Basic manipulation of GIF frames with magick

Thu, 13 Aug 2020 00:00:00 +0000

rOpenSci package or resource used

What did you do?

I demonstrate how you can use the magick package to do some basic manipulation of GIFs, such as playing it backwards, slowing some frame downs, and splicing in other frames.

URL or code snippet for your use case

Post on my blog

Image

Sector

List one of: academic / industry / government / non-profit / other

OSF: A Project Management Service Built for Research

Tue, 04 Aug 2020 00:00:00 +0000

osfr provides a (hopefully) convenient R interface to OSF (Open Science Framework, https://www.osf.io), a free service for managing research developed by the Center for Open Science (COS).

osfr completed its rOpenSci peer-review earlier this year and has been available on CRAN since February. Throughout its development and since its release I’ve had numerous conversations with members of the R community about OSF (and osfr), and through these interactions a couple recurring patterns emerged. First, it seems that many R users have heard of OSF but relatively few have first-hand experience with it. Second, I’m often asked how OSF compares to GitHub and whether it would even be useful for someone who already uses GitHub to manage their research.

Spanish and English blogs on how to use rtweet and magick

Sat, 01 Aug 2020 00:00:00 +0000

rOpenSci package or resource used

rtweet, magick

What did you do?

I like to use rtweet when I’m at conferences to look for impactful tweets and tweeters to follow or mute. I also enjoy using magick to add images to figures.

After a conference, I happened to sit next to two conference attendee and I showed them my R code and my analysis. They encouraged me to write a blog post about how to use this tool, so I wrote this blog post in English. Then I translated the human-readable parts of the code and published the blog in Spanish. I shared both blogs on Twitter and they were well received.

Creating a self-updating GitHub README using rtweet and GitHub Actions

Tue, 21 Jul 2020 00:00:00 +0000

rOpenSci package or resource used*

https://github.com/zhiiiyang/zhiiiyang/blob/af2921e2fe01cd59cab9138907f8da37ceabcb1d/script.R

What did you do?

After GitHub allows users to host their own README file on the profile page, people started to share many awesome README examples. Inspired by this tweet where Simon William used it to share his updates from blogs and commits, I created a README updating my latest tweet instead of having a static one by doing the following actions:

Use rtweet to get my latest tweet.
Use tweetrmd and webshot2 to turn the tweet into a screenshot. The entire process is deployed on GitHub using GitHub Actions templates from my friend Malcolm Barrett.

URL or code snippet for your use case*

Extraindo tabelas de documentos pdf em R com Tabulizer

Mon, 20 Jul 2020 00:00:00 +0000

rOpenSci package or resource used

Tabulizer

What did you do?

Estava procurando dados sobre operações de Garantia da Lei e da Ordem (GLOs) no Brasil para o artigo final de uma disciplina do doutorado. Infelizmente não há muita informação disponível em série histórica, apesar do Ministério da Defesa ter contabilizado alguns dados das operações realizadas desde 1992. Eles estão disponíveis aqui, assim com a metodologia usada para coleta-los. Maravilha, mas temos um problema: os dados não estão em planilhas prontas para gente usar, mas em pdf. Em dois pdfs, no caso. Um primeiro contendo variáveis como data , nome , local , missão e tipo da operação, e um segundo contendo o seu custo e o efetivo empregado. Resolvi então escrever um post mostrando um pouco o processo de extração e transformação inicial dos dados.

CRAN Checks API News: Documentation, Notifications, and More

Thu, 16 Jul 2020 00:00:00 +0000

In October last year we wrote about the CRAN Checks API (https://cranchecks.info). Since then there have been four new major items introduced: documentation, notifications, search, and a new version of the cchecks R package. First, an introduction to the API for those not familiar.

CRAN Checks API

The CRANS checks API was born because whilst being crucial to a package’s fate on CRAN, CRAN checks results were not available in a machine readable format, contrary to checks from continuous integration services. Indeed, CRAN checks results are only distributed as HTML pages. Therefore CRAN checks API’s goal is to provide data from CRAN checks in a format that’s easier to work with from code.

Community Captioning of rOpenSci Community Calls

Wed, 15 Jul 2020 00:00:00 +0000

Webinars and community calls are a great way to gather many people to discuss a specific topic, without the logistic hurdles of in-person events. But whether online or in-person, to reach the broadest audience, all events should work towards greater accessibility. In particular, it is difficult for people who are deaf or hard of hearing to follow the conversation because of low quality video hindering lip reading, or for non-native speakers because of low quality sound.

Maintaining an R Package - Community Call Summary

Tue, 14 Jul 2020 00:00:00 +0000

In March we held a Community Call discussing the maintenance of R packages. This call included a starting presentation by Julia Silge followed by a discussion featuring panelists with a wide variety of backgrounds: Elin Waring, Erin Grand, Leonardo Collado-Torres and Scott Chamberlain.

The rOpenSci Package Maintenance Community Call was my (Janani’s) first Community Call and I loved it. For R/software-dev newbies, learning the right terminology/lingo/vocabulary is everything. It can take a few dozen blog posts and many hours of reading before beginners get to the ‘aha’ moment of ‘oh, these are the terms I need to use to search for what I’m thinking!’. As there are many online resources out there, the default expectation is that one can search for and learn almost everything provided one knows the right keywords. There’s nothing like hearing a lively technical banter of experts to pick up the vernacular that one can easily build upon. The first-hand tips and tricks, do’s and don’ts, personal anecdotes of what worked beautifully and what crashed terribly, offered by years of experience are yet unmatched in bringing newbies into speaking the community’s language. That is the precise gap filled in by the timely and helpful rOpenSci Package Maintenance Community Call!

rOpenSci Ozunconf19

Fri, 10 Jul 2020 17:00:00 +0000

Watch https://ozunconf19.ropensci.org/ for updates

useR! 2020

Thu, 09 Jul 2020 20:00:00 +0000

Two members of our team will give talks at useR! 2020.

A better way to manage your Github personal access tokens

Tue, 07 Jul 2020 00:00:00 +0000

We have been working hard behind the scenes on the upcoming release of our new git package named gert, a joint effort from rOpenSci and the Tidyverse team. One of the main features of gert is the out-of-the-box authentication mechanism, which is provided via the new credentials package.

Among other things, the credentials package makes it possible to save and load https authentication details from the git credential store, which is part of the official command-line git. Thereby credentials are automatically shared between command line git and the gert package, while safely stored by your operating system’s preferred password manager.

Filtering pdfs using RegEx in their body

Thu, 25 Jun 2020 00:00:00 +0000

rOpenSci package or resource used*

What did you do?

I used pdftools to scan a large number of pdfs from a folder, and then stringr::str_which() to search the body of each pdf for any RegEx expression you want. Pdfs with matching RegEx expressions are saved in a new folder of your choosing.

URL or code snippet for your use case*

pdf_selector<-function(file_folder,new_folder,search_pattern){ library(pdftools) library(tidyverse) setwd(file_folder) dir.create(new_folder) filenames<-list.files(file_folder,pattern="*.pdf",full.names=TRUE) pdfs<-lapply(filenames,pdf_text)%>% lapply(paste,sep=" “,collapse=” “) l<-lapply(pdfs,str_which,pattern=search_pattern)%>% as.logical()%>% replace_na(FALSE) sapply(filenames[l],file.copy,to=new_folder) }

Using qualtRics to study the effect of COVID-19 on scientists

Sun, 21 Jun 2020 00:00:00 +0000

rOpenSci package or resource used*

qualtRics

What did you do?

Used in the workflow for analyzing a survey about how scientists have been affected by the COVID-19 pandemic
This also inspired a blog post with some tips for working with data collected through Qualtrics

URL or code snippet for your use case*

2 Months in 2 Minutes - rOpenSci News, June 2020

Thu, 18 Jun 2020 00:00:00 +0000

rOpenSci HQ

The rOpenSci team, together with ten expert community members, put together a post: When Field or Lab Work is not an Option - Leveraging Open Data Resources for Remote Research. We highlighted examples of how specific collections of packages are being used right now in fields as varied as archaeology and climate science and compiled a table of > 100 rOpenSci packages for access to open data.

Software Peer Review

Software peer review is accepting submissions again, after a pause to reduce the load on reviewers and editors in light of the COVID-19 crisis.

Using DataPackageR to create data package Pandemic Papers with Chris Knox

Wed, 17 Jun 2020 00:00:00 +0000

rOpenSci package or resource used

DataPackageR

What did you do?

Used DataPackageR to create a data package of the New Zealand Government’s released Covid-19 document dump available as searchable plain text.

Use case from from Chris Knox’s tweet

URL or code snippet for your use case

Output: Pandemic Papers Data Package GitHub

Sector

Other

Field(s) of application

Journalism

Testing an API wrapper with webmockr and vcr

Tue, 09 Jun 2020 00:00:00 +0000

rOpenSci package or resource used*

webmockr and vcr with the HTTP testing book. A question on rOpenSci discourse helped me discover the tools.

What did you do?

I tested the dev.to api wrapper I wrote. I used webmockr to create stubs to the apis, and vcr to record the API response to a local disk for testing purposes. I wrote it up here.

URL or code snippet for your use case*

My code is on GitHub

US lawmakers on Twitter during a pandemic: some corpus linguistics methods

Tue, 09 Jun 2020 00:00:00 +0000

rOpenSci package or resource used*

https://www.jtimm.net/2020/05/26/corp-comp-ling-covid19/

What did you do?

A short course in computational-corpus linguistics. A look at how US lawmakers have been tweeting about things COVID-19 since March. Semantic spaces, network graphs, and some politicization of COVID-concepts – for good measure. ++Techniques for working with multi-word expressions in text analytic workflows.

URL or code snippet for your use case*

Image

Sector

Academic

Create a time-lapse video using av package

Mon, 08 Jun 2020 00:00:00 +0000

rOpenSci package or resource used*

What did you do?

I took a series of photos with my DSLR and a tripod using an intervalometer.

Exposure Time: 13s
Aperture Value: F8
ISO: 100

Then it was employed #rstats to create the time-lapse, without install another software. The #av package facilitates this work. This is my window view in Santa Maria-Brazil. Car lights painting the night during COVID-19 times.

URL or code snippet for your use case*

Here you can find the code https://github.com/MauricioCely/time-lapse

Scrape an image from DeepZoom with R and magick, recomposing a single image from multiple tiles

Mon, 08 Jun 2020 00:00:00 +0000

rOpenSci package or resource used*

What did you do?

DeepZoom allows webmasters to display high resolution images in an online viewer. It mostly discourages downlading the original high resolution images to your local drive. Magick combined with rvest can be used to get these images nevertheless with the help of R.

Full code for doing so is presented on my blog on mapping and data mining

In the core of the code, I use the magick R package to recompose the whole image from the tiles. This in two embedded for-loops. The recomposing magic happens in the line

Superior svg graphics rendering in R, and why it matters

Thu, 28 May 2020 00:00:00 +0000

This week we released a major new version of the rsvg package on CRAN. This package provides R bindings to librsvg2 which is a powerful system library for rendering svg images into bitmaps that can be displayed, or use for further processing in for example the magick package.

The biggest change in this release is the R package on Windows and MacOS now includes the latest librsvg 2.48.4. This is a major upgrade; the librsvg2 rendering engine has been completely rewritten in Rust ¹ using components from Mozilla Servo. This has resulted in major improvements in quality and performance, and we have gained full support for css styling.

Detecting the Effects of Sustained Glacier Wastage on Streamflow in Variably Glacierized Catchments (Using tidyhydat)

Mon, 25 May 2020 00:00:00 +0000

rOpenSci package or resource used*

tidyhydat

What did you they do?

This study focused on the effects of glacier melt on streamflow in the Canadian portion of the Columbia River headwaters over the period 1977 to 2017. Between 1985 and 2013, glacier coverage decreased by up to 2% of catchment area for the 35 study catchments. The analyses suggest that glacier-melt reductions have exacerbated a regional climate-driven trend to decreased August streamflow contributions from unglacierized areas.

Using {drake} for machine learning

Fri, 22 May 2020 00:00:00 +0000

rOpenSci package or resource used*

https://edwinth.github.io/blog/drake-ml/

What did you do?

I elaborated on how I use {drake} to create machine learning products end-to-end, using it in combination of the R package structure.

URL or code snippet for your use case*

Sector

industry

When Field or Lab Work is not an Option - Leveraging Open Data Resources for Remote Research

Tue, 19 May 2020 00:00:00 +0000

The COVID-19 pandemic has dramatically impacted all of our lives in a very short period of time. Spring and summer are usually very busy as students prepare to go the field to engage in various data collection efforts. The pandemic has also disrupted these carefully planned activities as travel is suspended and local and remote field stations have closed indefinitely. A lost field season can be a major setback for a dissertation timeline and students will have to improvise. One promising opportunity to continue research efforts during these unprecedented times is taking advantage of the massive amounts of open scientific data that are freely available. Open data can form the basis of a review, synthesis, or new research.

bomrang with a third party package, stationaRy, to get hourly weather data and clifro to plot wind roses

Sun, 17 May 2020 00:00:00 +0000

rOpenSci package or resource used

bomrang, clifro

What did you do?

We had an issue with an on-site weather station where the wind-vane was not properly calibrated. So we opted to use BOM data to check wind directions during the rainfall events in which we were measuring fungal spore dispersal to make sure the wind was blowing roughly in the direction of our trap plants.

We used bomrang’s sweep_for_stations() to identify stations within a given radius of a site where we had research plots to then download hourly weather data using the stationaRy package (bomrang does not offer hourly weather data).

Package for downloading shapefiles using piggyback

Mon, 11 May 2020 00:00:00 +0000

rOpenSci package or resource used*

piggyback

What did you do?

I created a package called {leaidr} to use facilitate the download and use of U.S. school district shapefiles. The shapefile is over GitHub’s allowed limit of 100MB. Originally, I tried to use GitHub LFS as a way to upload the file. Unfortunately, GitHub LFS is not reproducible in that when others download the package, they wouldn’t be able to access the file.

A Roundup of R Tools for Handling BibTeX

Thu, 07 May 2020 00:00:00 +0000

Our website is based on Markdown content rendered with Hugo. Markdown content is in some cases knit from R Markdown, but with less functionality than if one rendered R Markdown to html as in the blogdown default. In particular, we cannot use the usual BibTex + CSL + Pandoc-citeproc dance to handle a bibliography. Thankfully, using the rOpenSci package RefManageR, we can still make our own bibliography from a BibTeX file without formatting references by hand. In this post we shall present our custom workflow for inserting citations, as well as more mainstream tools.

Visualize covid19 cases using rnaturalearth package

Tue, 05 May 2020 00:00:00 +0000

rOpenSci package or resource used*

rnaturalearth

What did you do?

I created several R dataset packages for tracking the covid19 virus in different geographic locations (Italy, Switzerland, etc.). To help users create choropleth maps with a minimum effort I added for each dataset (when applicable) a column with the corresponding region/province naming convention used in the rnaturaleath package. The goal is to enable a seamless merge of the data with the geospatial data available in the package with the ne_state function.

{drake} at Queensland Fire and Emergency Services

Mon, 04 May 2020 00:00:00 +0000

rOpenSci package or resource used*

https://milesmcbain.xyz/the-drake-post/

What did you do?

I wrote a blog post detailing how my team of 4 data scientists at Queensland Fire and Emergency Services sets up our R projects with {drake}. I also talk a little bit about how it facilitates colloboration and debugging.

URL or code snippet for your use case*

Sector

Government

Field(s) of application

Sofware Engineering

Highlights of Hugo Code Highlighting

Thu, 30 Apr 2020 00:00:00 +0000

Thanks to a quite overdue update of Hugo on our build system¹, 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 highlighting).

Make your code look pretty

If you notice and appreciate the difference between

Using taxadb to query taxonomic information in ecology projects

Mon, 27 Apr 2020 00:00:00 +0000

rOpenSci package or resource used*

taxadb

URL or code snippet for your use case*

https://gavinmasterson.netlify.app/post/taxadb/

Image

Sector

academic

Field(s) of application

ecology, conservation, evolutionary biology, species distribution modeling

What did you do?

I used the {taxadb} package to verify taxonomic information for two ecology-related projects. In the second case, I compared taxonomic identifications from 2006 with the current information for those species to identify changes in name and/or status..

Miscellaneous Wisdom about R Markdown & Hugo Gained from Work on our Website

Thu, 23 Apr 2020 00:00:00 +0000

Whilst working on the blog guide, Stefanie Butland and I consolidated knowledge we had already gained, but it was also the opportunity to up our Rmd/Hugo technical game. Our website uses Hugo but not blogdown¹ to render posts: every post is based on an .md file that is either written directly or knit from an .Rmd file. We wanted to provide clear guidance for both options, and to stick to the well-documented Hugo way of e.g. inserting figures. We also wanted to provide post contributors with an as smooth as possible workflow to create a new post. Working on this mission, unsurprisingly we learned a lot, and why not share our newly acquired technical know-how? In this post I shall go through four things we learned about Rmd/Hugo, while trying to provide context about the why of our using them.

Animated generative art with magick

Tue, 21 Apr 2020 00:00:00 +0000

This use case for {magick} was inspired by the ‘ashtree’ algorithm by Danielle Navarro. I thought it would be really nice to show the organic growth of the trees. The tree itself is a result of a branching process, an excellent example for some simple generative art using functional programming. The animation can be admired here.

rOpenSci package or resource used

https://gist.github.com/psolymos/f0f8132ee03b6f7f03e275473b355b8e

URL or code snippet for your use case

Automatic Code Cleaning in R with Rclean

Tue, 21 Apr 2020 00:00:00 +0000

Leave the code cleaner than you found it.

– R.C. Martin in Clean Code

The R language has become very popular among scientists and analysts because it enables the rapid development of software and empowers scientific investigation. However, regardless of the language used, data analysis is usually complicated. Because of various project complexities and time constraints, analytical software often reflects these challenges. “What did I measure? What analyses are relevant to the study? Do I need to transform the data? What’s the function for the analysis I want to run?” Although many researchers see the value in learning to write software, the time investment for learning a programming language alone is still exceedingly high for many, let alone also learning software best practices. The downside to the rapid spread of data science is that learning to create good software takes a back-seat to just writing code that will get the job “done” leading to issues with transparency and software that is highly unstable (i.e. buggy and not reproducible).

2 Months in 2 Minutes - rOpenSci News, April 2020

Fri, 17 Apr 2020 00:00:00 +0000

rOpenSci HQ

The recording, collaborative notes and links to community discussion and resources are up for our latest Community Call on Maintaining an R package. Panel moderated by Julia Silge included Elin Waring, Erin Grand, Leonardo Collado-Torres, and Scott Chamberlain.

Software Peer Review

1 staff-contributed package passed software peer review.

parzer - Parse messy geographic coordinates. Author: Scott Chamberlain; Reviewers: Julien Brun, María Victoria Munafó; Read the Review

On March 16, we paused new submissions for software peer review for 30 days (possibly longer) in the interest of reducing load on reviewers and editors in light of the COVID-19 crisis.

Extracting eBird Data from a Polygon

Thu, 16 Apr 2020 00:00:00 +0000

One of the first things I took on when I started at the Cornell Lab of Ornithology was creating the auk R package for accessing eBird data. The entire eBird dataset can be downloaded as a massive text file, called the eBird Basic Dataset (EBD), and auk pulls out manageable chunks of the dataset based on various spatial, temporal, or taxonomic filters. I’m often asked “how do I extract data from within a polygon?” (usually “polygon” is replaced by “shapefile”, but I try to avoid that word since there’s good reasons to stop using shapefiles). Rather than answer these questions individually, I thought I’d do a quick post about how to do this with auk. Note that, at the time of posting, this requires auk version 0.4.1 or higher, which can be installed with:

Use of crul's retry sub-routine in an API package

Thu, 16 Apr 2020 00:00:00 +0000

rOpenSci package or resource used*

crul

URL or code snippet for your use case*

Link to a blog post, a gist, or an academic paper, or provide some code inline

Sector

List one of: academic / industry / government / non-profit / other

rOpenSci Dev Guide 0.4.0: Updates

Tue, 14 Apr 2020 00:00:00 +0000

rOpenSci Software Peer Review’s guidance has been compiled in an online book for more than one year now. We’ve just released its fourth version. To find out what’s new in our dev guide 0.4.0, you can read the changelog, or this blog post for more digested information.

Note that, as indicated in the README of the software review repo, in the interest of reducing load on reviewers and editors as we manage the COVID-19 crisis, rOpenSci is temporarily pausing new submissions for software peer review for 30 days (and possibly longer). Please check back in the software review repository again after 17 April for updates. In this period new submissions will not be handled, nor new reviewers assigned. Reviews and responses to reviews will be handled on a ‘best effort’ basis, but no follow-up reminders will be sent.

{Magick}ally Visualize Historical Google Maps Traffic Data

Fri, 10 Apr 2020 00:00:00 +0000

rOpenSci package or resource used

https://e.olamijuwon.com/how-to-magickally-visualize-historical-google-maps-traffic-data/

URL or code snippet for your use case

Image

Sector

Other

Field(s) of application

Social sciences

What did you do?

I used {magick} in combination with {googleway} package to visualize historical road traffic in three major cities in South Africa. This exercise was motivated by the increased need to evaluate compliance with social distancing as many African countries enforce full/partial lock down in the wake of COVID-19. Unfortunately, Google Maps does not provide historical traffic data beyond traffic information on a typical (specified) day and time.

10 Things We Learned in Creating the Blog Guide with bookdown

Tue, 07 Apr 2020 00:00:00 +0000

After soliciting, reviewing, and publishing over 100 blog posts and tech notes by rOpenSci community members, we have created the rOpenSci Blog Guide for Authors and Editors to address many frequently asked questions and frequently given suggestions.

Technically, we structured the content as a bookdown gitbook. It was Stef’s first foray into the glorious process of publishing a book with bookdown, and Maëlle’s second¹. And oh, we learned a lot.

Stef (first-timer)

1. How to collaborate across timezones

There is a 9-hour time difference between Maëlle and me for most of the year. I’m in Kamloops, Canada and Maëlle is in Nancy, France. Since so much of this is new to me, text-based explanations from Maëlle via Slack usually boggled my mind. It helped immensely to have a weekly 30-minute meeting (8:30am for Stef and 5:30pm for Maëlle) with agenda and notes in a shared google doc. We would talk through our approaches and priorities and Maëlle would coach me in new-to-me tools.

pdftools for parsing tables from many .pdfs

Tue, 31 Mar 2020 00:00:00 +0000

rOpenSci package or resource used*

pdftools

URL or code snippet for your use case*

Link to GitHub repo
- Has all the code and raw PDFs for users to test out themselves
Vignette/Webpage with example code run

Image

Raw example of the PDF table from the TTB. Notice there are inconsistent spaces between the table columns.

Sector

Finance, econometrics

Field(s) of application

Forecasting, finance, econometrics, but really could be used for anything!

Searching Microsoft Academic & extracting the metadata

Fri, 27 Mar 2020 00:00:00 +0000

rOpenSci package or resource used*

microdemic

What did you do?

My exercise comprise a piece of code that can help to search the articles and extract the metdata from Microsoft Academic. The example is limited with only one query type. microdemic

COVID March publications

The query consists of the words (terms) and the publication date range. Number of results were received via ma_calchist, the records were extracted by 100 with ma_evaluate. The guy who learned me to test this was Darrin Eide

parzer: Parse Messy Geographic Coordinates

Thu, 19 Mar 2020 00:00:00 +0000

parzer is a new package for handling messy geographic coordinates. The first version is now on CRAN, with binaries coming soon hopefully (see note about installation below). The package recently completed rOpenSci review.

parzer motivation

The idea for this package started with a tweet from Noam Ross (https://twitter.com/noamross/status/1070733367522590721) about 15 months ago.

The idea being that sometimes you have geographic coordinates in a messy format, or in many different formats, etc. You can think of it as being the package for geographic coordinates that lubridate is for dates.

Maintaining an R Package

Wed, 18 Mar 2020 00:00:00 +0000

satRday Neuchâtel

Sat, 14 Mar 2020 08:00:00 +0000

Mark Padgham, rOpenSci Software Research Scientist, is giving a talk at satRday Neuchâtel. Community member and package maintainer, Sina Rüeger, is one of the organizers.

This is a remote conference. Free with registration.

Supercharge your GitHub Actions Experience with tic

Fri, 13 Mar 2020 00:00:00 +0000

“Continuous Integration” (CI) has become a standard for proper software development. Checking the integrity of software after changes have been made is essential to ensure its proper functionality. Also, CI helps catch problems introduced by dependencies early when executed on a regular basis (usually done via scheduled CRON runs).

Multiple professional providers exist (Travis CI, AppVeyor CI, Circle CI, etc.) which offer CI services to the public. Most services offer limited free build contingents for open-source projects. However, it has not been easy for the R community to jump on the train right away as most providers did not support the R language natively on their side. Therefore, the R community started to create their own configurations to quickly automate the checking of R packages on Travis CI. In fact, the first commit of the official r.rb build script was made on Feb 1st 2015 by Craig Citro. Since then 21 unique contributors have maintained this configuration under the meta-lead of Jim Hester and Jeroen Ooms which allowed many thousands of R package maintainers to jump onto the train.

Community Call - Maintaining an R Package

Wed, 04 Mar 2020 00:00:00 +0000

For this Community Call, we’re trying something different. We’ll start with a short talk by Julia Silge, then spend most of the time on Q & A with four panelists - Elin Waring, Erin Grand, Leonardo Collado-Torres, and Scott Chamberlain - moderated by Julia.

Our panelists bring a wide range of perspectives so there’s something for everyone. Collectively, they have experience developing and maintaining passion-project packages, very popular packages, too many packages on CRAN, packages on Bioconductor, and taking over maintenance (and changing things!) of a package developed by someone else.

opentripplanner: Fast and Easy Multimodal Trip Planning in R with OpenTripPlanner

Tue, 25 Feb 2020 00:00:00 +0000

With services like Google Maps, finding the fastest route from A to B has become quick, cheap, and easy. Not just for driving but walking, cycling and public transport too. But in the field of transport studies, we often want not only a single route, but thousands or millions of routes. This is where we hit a problem for services such as Google or the Open Route Service, that usually only allow a limited number of free routes per day (typically around 1000). So routing is either very time consuming or expensive. Another problem is that we may not be interested in the current travel options, but how those options may change in the future. Such as, after a new bridge has been built or a new bus timetable has been introduced. Therefore, researchers can find it useful to run their own routing services where they have more control and can produce as many routes as necessary.

rOpenSci's Leadership in #rstats Culture

Fri, 21 Feb 2020 00:00:00 +0000

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. At rstudio::conf, I was surrounded by so many of the incredible people I had met at that very same runconf15. These folks are visionaries and leaders, founding and leading global efforts in open source software and inclusive culture, and the fact that they were all together at a small event convened by rOpenSci holds great significance. I am so honored to know this community, and to consider them allies and friends. The RStudio Conference (“rstudio::conf”), a conference with 2400 people, felt cozy with their presence and with the visible efforts they have led to make R and beyond a welcoming, innovative space. In a follow-up to an earlier blog summary of rstudio::conf(2020), here I want to reflect on how important runconf15 was, and how truly unique and gamechanging rOpenSci is.

2 Months in 2 Minutes - rOpenSci News, February 2020

Thu, 20 Feb 2020 00:00:00 +0000

rOpenSci HQ

On behalf of rOpenSci, thank you to everyone who has contributed their creativity, curiosity, smarts, and time in the last year. Read our Thank You, 2019.

Software Peer Review

3 community-contributed packages passed software peer review.

osfr - R Interface to OSF. Author: Aaron Wolen; Reviewers: Heidi Seibold, Carl Boettiger; Read the Review

pdftools for parsing .pdf from a URL - public data mining

Sat, 15 Feb 2020 00:00:00 +0000

rOpenSci package or resource used*

https://www.ecologi.st/post/weather/

URL or code snippet for your use case*

library(httr) # will be use to make HTML GET and POST requests
library(rvest) # will be used to parse HTML
library(tidyverse) # data munge
library(pdftools) # parse pdf

# |- data ----
library(httr) # will be use to make HTML GET and POST requests
library(rvest) # will be used to parse HTML
library(tidyverse) # data munge
library(pdftools) # parse pdf

# |- data ----
url <- "https://www.bsee.gov/guidance-and-regulations/guidance/safety-alerts-programs"

r <- GET(url)

raw_tbl <- r %>%
 content() %>%
 html_node("table") %>%
 html_table() %>%
 as_tibble() %>%
 janitor::clean_names()

raw_tbl

# |- munge ----
normalize_title <- function(title) {
 title %>%
 tolower() %>%
 str_replace_all("\\b\\s\\b", "\\-") %>%
 str_remove_all("\\s")
}

clean_tbl <- raw_tbl %>%
 mutate(norm_url = map_chr(title, normalize_title))

clean_tbl$norm_url[[1]]

base_url <- "https://www.bsee.gov/sites/bsee.gov/files/safety-alerts//"

ReadPDF <- function(base_url, pdf_url) {
 pdf_url <- glue::glue(base_url, {pdf_url}, ".pdf")

 print(pdf_url)

 # pdftools time!
 pdf_text(pdf_url)
}

SafeReadPDF <- possibly(ReadPDF, NA)

SafeReadPDF(base_url, clean_tbl$norm_url[[1]])

Image

taxadb: A High-Performance Local Taxonomic Database Interface

Thu, 13 Feb 2020 00:00:00 +0000

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. One potentially powerful approach for addressing these issues is to resolve scientific names to taxonomic identifiers that follow a consistent taxonomic concept. In such a workflow, data from one of the many taxonomic providers (e.g. Integrated Taxonomic Information System ¹, Catalogue of Life ², National Center for Biological Information ³) is integrated with biodiversity datasets to identify an accepted ID for each name. Multiple tools exist to facilitate this workflow, including R’s taxize package ⁴, which provides an API interface to taxonomic databases. However, due to the nature of API queries which are slow, limited in scope, and dependent on the current state of the database, it remains difficult to resolve names to a taxonomic authority in quick, reproducible way. taxadb seeks to address these issues using a new approach for interfacing with taxonomic data via a local database of taxonomic providers.

osmdata use case: Wall Art

Thu, 06 Feb 2020 00:00:00 +0000

rOpenSci package or resource used*

osmdata

URL or code snippet for your use case*

This github repository by Dean Marchiori

Image

What did you do?

Dean Marchiori used the osmdata package to create a striking image which he printed and hung on a wall. His code to reproduce the image is contained with the github repository file culburra.Rmd.

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

Wed, 05 Feb 2020 00:00:00 +0000

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.

An rOpenSci unconference (unconf) is about building - building software, tools, but more importantly community. It operates on the premise that we all belong.

Working with audio in R using av

Mon, 03 Feb 2020 00:00:00 +0000

The latest version of the rOpenSci av package includes some useful new tools for working with audio data. We have added functions for reading, cutting, converting, transforming, and plotting audio data in any popular audio / video format (mp3, mkv, aac, etc).

The functionality can either be used by itself, or to prepare audio data for further analysis in R using other packages. We hope this clears an important hurdle to use R for research on speech, music, and whale mating calls.

tabulizer for parsing block-text from .pdf

Sat, 01 Feb 2020 00:00:00 +0000

rOpenSci package or resource used*

tabulizer

URL or code snippet for your use case*

Goal: extract certain block of data from different sections of the .pdf

Strategy: use split-apply-combine approach via locate_areas() (to get box coordinates of sections of interest) and then extract_tables() to get the data with the section.

locate_areas() demo

Code snippet

# |- fxn ----
# data munge function for map() later
CleanHeader <- function(tbl) {
 tbl %>%
 tidyr::pivot_longer(
 cols = -idx
 ) %>%
 dplyr::group_by(name) %>%
 dplyr::filter(value != "") %>%
 dplyr::summarise(value = paste0(value, collapse = ":")) %>%
 tidyr::separate(value, c("cat", "data"), sep = ":", extra = "merge") %>%
 dplyr::mutate_at(vars(data), stringr::str_remove, ":") %>%
 dplyr::select(cat, data)
}

# |- data ----
file <- "./ropensci_white.pdf"

# get the box coordinates via interactive selection; this info is then used in extract_tables() area args
locate_areas(file, pages = 1)

# extract data
header_raw <- extract_tables(f, pages = 1,
 area = list(c(74, 88, 128, 522)),
 guess = FALSE)

# data munge; data/application specific
header_raw[[1]] %>%
 tibble::as_tibble() %>%
 janitor::remove_empty("cols") %>%
 dplyr::mutate(idx = cumsum(stringr::str_detect(V1, "Section Marker"))) %>%
 dlpyr::group_split(idx) %>%
 purrr::map_dfr(CleanHeader)

Image

Sample .pdf where coloured boxes represent sections of interest to extract data from.

Accessing, wrangling and plotting global weather data (for free!)

Thu, 30 Jan 2020 00:00:00 +0000

rOpenSci package or resource used*

rnoaa, lawn

URL or code snippet for your use case*

Image

Sector

academic

Field(s) of application

ecology, climatology, meteorology

What did you do?

Search, extract, wrangle and plot weather data from NOAA’s archives using South Africa as a use case. This is particularly valuable for South Africa because our national weather service charges for their data. Thanks @sckottie and others that have contributed to these packages!

Call BEAST2 for Bayesian evolutionary analysis from R

Tue, 28 Jan 2020 00:00:00 +0000

babette ¹ is a package to work with BEAST2 ², a software platform for Bayesian evolutionary analysis from R.

babette is a spin-off of my own academic research. As a PhD I work on models of diversification: mathematical descriptions of how species form new species. Instead of working on a species' individuals, I work on species as evolutionary lineages. A good way to show the evolutionary relationships between species are phylogenies. For example, this is a phylogeny, with four species, eloquently named ‘1’, ‘2’, ‘3’ and ‘4’:

mapping the location of biogeography researchers with `refsplitr`

Tue, 28 Jan 2020 00:00:00 +0000

rOpenSci package or resource used

package refsplitr

URL for use case

Eichhorn, M. P, Baker, K., & Griffiths, M. (2019). Steps towards decolonising biogeography. Frontiers of Biogeography . http://dx.doi.org/10.21425/F5FBG44795 Retrieved from https://escholarship.org/uc/item/2k00787j.

Image

An image from the authors’ blog post about the paper; the map of author locations was generated with refsplitr .

Sector

academic

Field(s) of application

biogeography, ecology, bibliometrics, scientometrics

rOpenSci 2019 Code of Conduct Transparency Report

Thu, 16 Jan 2020 00:00:00 +0000

In January 2019, we announced the release of rOpenSci’s Code of Conduct version 2.0. This includes a named Committee, greater detail about unacceptable behaviors, instructions on how to make a report, and information on how reports are handled. We are committed to transparency with our community while upholding of victims and people who report incidents.

Our Code of Conduct applies to all people participating in the rOpenSci community, including rOpenSci staff and leadership. It applies to all modes of interaction online including GitHub project repositories, the rOpenSci discussion forum, Slack, Community Calls, and in person at rOpenSci-hosted events or events officially endorsed by rOpenSci, including social gatherings affiliated with an event.

rOpenSci Code of Conduct Annual Review

Thu, 16 Jan 2020 00:00:00 +0000

One year ago, we released our new Code of Conduct. At that time, the Code of Conduct Committee (authors of this post) agreed to do an annual review of the text, reporting form, and our internal guidelines.

We have made one change to the Code of Conduct text. Because some people who have experienced abuse prefer not to label themselves as a victim, in “We are committed to transparency with our community while upholding the privacy of victims” we edited to “… upholding the privacy of victims and people who report incidents”.

Thank You, 2019

Mon, 23 Dec 2019 00:00:00 +0000

We mean it.

On behalf of rOpenSci, thank you to everyone who has contributed their creativity, curiosity, smarts, and time in the last year. We are fortunate to have paid staff who work to build technical and social infrastructure to lower barriers to working with research data. But it is our community, built on trust, that binds us together and helps us see who we are working for.

Many people have submitted their R packages for software peer review (31)¹, reviewed those packages (~60), contributed some code or documentation to a package (117 people made their first code contribution to rOpenSci this year), (co-)authored a blog post or tech note about their package or an rOpenSci resource (48 authors), shared a use case to help package authors see how their work is being used and help other users imagine how they can apply it (26 people), attended a Community Call (331 people in 23 countries), cited our software (306 citations of 122 packages), asked or answered questions, explored project ideas, or gave us a generous shoutout in a talk, a post, or on Twitter.

Want to Intern with rOpenSci’s Community Manager?

Mon, 23 Dec 2019 00:00:00 +0000

Want to get some hands-on insights into running an open source community? Here’s an opportunity to work with me, rOpenSci’s Community Manager, on some non-code community-related work. I am looking for someone to work 1 day a week for 12 to 14 weeks.

Working alongside rOpenSci’s Community Manager, Stefanie Butland, you will use guidelines and checklists to help run some of our established programs like our Blog and Community Calls. Tasks include:

Reviewing and editing community-contributed blog posts via Git and GitHub, publishing them to our website, and drafting and scheduling tweets to promote them
Publishing information on upcoming Community Calls to the rOpenSci website, promoting them through multiple channels, and post-Call video editing
Monitoring social media for use cases of rOpenSci packages or resources, encouraging people to share those in our public forum, and scheduling tweets to promote them
Drafting and scheduling tweets when an rOpenSci package is featured in RViews Top 40, highlighted in R-Weekly monthly news, or similar digests
Sharing your opinions with us on how we can improve any of these

Who are you? You are familiar with R communities, understand that it’s people that make software, and you have a sense of community building with a “what’s it like to be you” perspective. You have a working knowledge of Git and GitHub, are skilled in written and spoken communication, grammar, and editing in English and are comfortable communicating on Twitter.

2 Months in 2 Minutes - rOpenSci News, December 2019

Fri, 20 Dec 2019 00:00:00 +0000

rOpenSci HQ

rOpenSci Announces a New $896k Award From The Gordon and Betty Moore Foundation to Improve the Scientific Package Ecosystem for R.
We’re excited to announce a new member of our team! Introducing Mark Padgham, rOpenSci’s new Software Research Scientist
NumFOCUS recognizes Melina Vidoni and Will Landau for their contributions to rOpenSci.
Videos, speaker’s slides, resources and collaborative notes from our Community Call on Testing in R are posted.
What would you like to hear about in an rOpenSci Community Call? We are soliciting your emoji-votes and new ideas for Community Call topics and speakers.

We cleaned our website URLs with R!

Thu, 19 Dec 2019 00:00:00 +0000

Last year we reported on the joy of using commonmark and xml2 to parse Markdown content, like the source of this website built with Hugo, in particular to extract links, at the time merely to count them. How about we go a bit further and use the same approach to find links to be fixed? In this tech note we shall report our experience using R to find broken/suboptimal links and fix them.

HTTP testing in R: overview of tools and new features

Wed, 11 Dec 2019 00:00:00 +0000

Testing is a crucial component to any software package. Testing makes sure that your code does what you expect it to do; and importantly, makes it safer to make changes moving forward because a good test suite will tell you if a change has broken existing functionality. Our recent community call on testing is a nice place to get started with testing.

One way to make testing even harder is through including HTTP requests. This adds complexity for many reasons:

How to precompute package vignettes or pkgdown articles

Sun, 08 Dec 2019 00:00:00 +0000

Read it in: Español.Read it in: Português.

As of earlier this year, we are now automatically building binaries and pkgdown documentation for all rOpenSci packages. One issue we encountered is that some packages include vignettes that require some special tools/data/credentials, which are unavailable on generic build servers.

This post explains how to include such vignettes and articles in your package.

On package vignettes

By default, R automatically recreates vignettes during R CMD check or when generating pkgdown sites by running all R code. This is useful because it provides some extra testing of your code and ensures that documentation is reproducible. However, sometimes it is not a good idea to run the code on every build server, every time. For example:

Last Night, Testing Saved my Life

Wed, 04 Dec 2019 00:00:00 +0000

To the uninitiated, software testing may seem variously boring, daunting or bogged down in obscure terminology. However, it has the potential to be enormously useful for people developing software at any level of expertise, and can often be put into practice with relatively little effort.

Our 1-hour Call will include two speakers and at least 20 minutes for Q & A.

As someone with a background in science, not software engineering, Steffi LaZerte will share her experiences using automated testing in R to ensure that packages do what they’re supposed to do, on all the operating systems they’re supposed to do it on, and that they handle weird stuff gracefully.

Introducing Mark Padgham, rOpenSci’s new Software Research Scientist

Tue, 03 Dec 2019 00:00:00 +0000

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. He will work closely with Noam Ross, rOpenSci Leadership team member, and Scientist at EcoHealth Alliance and Karthik Ram, rOpenSci Project Lead.

Batch image manipulation using magick

Tue, 26 Nov 2019 00:00:00 +0000

rOpenSci package or resource used*

https://github.com/roryspanton/batch-magick

URL or code snippet for your use case*

Sector

Any

Field(s) of application

Cognitive psychology - or anything else with images!

What did you do?

I used magick in conjunction with functions from purrr (tidyverse) to manipulate and convert multiple images concisely and efficiently. This simple framework allows the user to read any number of images in magick supported formats, perform the same magick manipulations on all of them, and export them as different file types (if desired), with neat file names. This automates the potentially long and tedious process of performing the same manipulation on large sets of images.

rnassqs: accessing USDA agricultural data via API

Tue, 26 Nov 2019 00:00:00 +0000

The United States Deparment of Agriculture National Agricultural Statistics Service (USDA-NASS) provides a wide range of agricultural data that includes animal, crop, demographic, economic, and environmental measures across a number of geographies and time periods. This data is available by direct download or queriable via the Quick Stats interface. While the Quick Stats tool puts a large amount of data into the hands of users, the interface can be frustrating, especially when trying to access more than 50,000 records or hoping to automate downloading data when new data is released. I developed rnassqs as a solution to these frustrations. rnassqs provides a simple R interface for the Quick Stats API. By iterating over a set of parameters, R users can make processing NASS data reproducible and automated.

Analyzing invoice data from Elsevier relative to hybrid open access

Mon, 25 Nov 2019 00:00:00 +0000

Package or resource used

rcrossref, crminer, tabulizer

URL or code snippet for your use case* https://subugoe.github.io/scholcomm_analytics/posts/elsevier_invoice/

Sector Academic

Field(s) of application Scholarly Communications Analytics, Open Access Monitoring, Licensing in Libraries

What did you do?

I used several rOpenSci packages to mine Elsevier full-texts for invoice data relative to open access articles in hybrid journals. Such evidence is critical to keep track of funding streams for open access publications. Academic publishers rarely make publication fee spending for hybrid journals transparent. Surprisingly, Elsevier is a notable exception sharing this data.

NumFOCUS recognizes Melina Vidoni and Will Landau for their contributions to rOpenSci

Mon, 25 Nov 2019 00:00:00 +0000

rOpenSci thrives because of volunteer contributions from community members - submitting and reviewing R packages, serving as editors for software peer review, writing blog posts, sharing information about packages and resources, contributing code and documentation and answering others’ questions. Recently our fiscal sponsor, NumFOCUS, gave us an opportunity to nominate two contributors for recognition at the NumFOCUS annual summit. Sometimes all we can do is publicly express our gratitude for the people who help make our software robust and sustainable, and make our community a welcoming place that adds value to people’s experiences.

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

Thu, 14 Nov 2019 00:00:00 +0000

Studies of muscle physiology often rely on closed-source, proprietary software for not only recording data but also for data wrangling and analyses. Although specialized software might be necessary to record data from highly-specialized equipment, data wrangling and analyses should be free from this constraint. It’s becoming more common for researchers to provide code along with published papers (but usually as Matlab scripts…ugh), but it is still typical for most analyses to be performed with code that stays in-house. Even worse is when some of the steps are carried out in a non-reproducible way, like needing to click and drag sliders across a screen (by hand!!) to select a data range of interest.

Community Call - Last Night, Testing Saved my Life

Tue, 12 Nov 2019 00:00:00 +0000

Our 1-hour Call will include two speakers and at least 20 minutes for Q & A.

As someone with a background in science, not software engineering, Steffi LaZerte will share her experiences using automated testing in R to ensure that packages do what they’re supposed to do, on all the operating systems they’re supposed to do it on, and that they handle weird stuff gracefully.

ERDDAP servers use case: tidync and rerddap

Thu, 07 Nov 2019 00:00:00 +0000

rOpenSci package or resource used*

rerddap and tidync

URL or code snippet for your use case*

Original Post: https://twitter.com/u_ribo/status/1191685777660362752

Source Code: https://github.com/uribo/30DayMapChallenge/blob/45283ace68005542bcfa6a35c2a6910500c5f4fc/day5.R

Image

Field(s) of application

data visualization, spatial

What did you do?

NOAA SST observation data was searched and acquired with {rerddap}, and netCDF format files were processed and visualized with {tidync}.

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

Wed, 06 Nov 2019 00:00:00 +0000

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. Over the coming months we plan to roll out more tools and services to make it easier to maintain and distribute packages while capturing the impact of such work.

tidync: scientific array data from NetCDF in R

Tue, 05 Nov 2019 00:00:00 +0000

In May 2019 version 0.2.0 of tidync was approved by rOpenSci and accepted to CRAN. Here we provide a quick overview of the typical workflow with some pseudo-code for the main functions in tidync. This overview is enough to read if you just want to try out the package on your own data. The tidync package is focussed on efficient data extraction for developing your own software, and this somewhat long post takes the time to explain the concepts in detail.

Reproducible CV using rorcid

Sat, 02 Nov 2019 00:00:00 +0000

rOpenSci package or resource used

rorcid

Sector

Public relations

Field

Reproducible science

What did you do?

A curriculum vitae is really a set of lists. It would be fantastic to have a reproducible CV that capitalizes on R to re-populate works to a table. I examined the capacity of rorcid as a mechanism to scrape works from my ORCID profile, tidy a bit include filter to papers only for now, and then pull that table into an R Markdown and knit out a clean CV to pdf. Seems like a viable strategy. I co-tested wosr as an alternative. https://cran.r-project.org/web/packages/wosr/index.html Numerous advantages to rorcid package.

(Re)introducing skimr v2 - A year in the life of an open source R project

Tue, 29 Oct 2019 00:00:00 +0000

Theme song: PSA by Jay-Z

We announced the testing version of skimr v2 on June 19, 2018. After more than a year of (admittedly intermittent) work, we’re thrilled to be able to say that the package is ready to go to CRAN. So, what happened over the last year? And why are we so excited for v2?

Wait, what is a “skimr”?

skimr is an R package for summarizing your data. It extends tidyverse packages, and dplyr in particular, so that you can get a broad set of summary statistics with a single function call. You can install a pre-release version from the package’s GitHub repo.

tidyhydat and weathercan webinar

Tue, 29 Oct 2019 00:00:00 +0000

I hope this is approximately what is intended here:

Package or resource used*

tidyhydat, weathercan, hydrology task view

URL or code snippet for your use case*

https://cwra.org/en/introduction-to-r-webinar/

Sector

government presented; academic and industry attendants

Field(s) of application

hydrology, meteorology

What did you do?

I gave a 2 hours webinar for water professionals illustrating how one might use the tidyhydat and weathercan packages.

rmangal: making ecological networks easily accessible

Mon, 21 Oct 2019 00:00:00 +0000

In early September, the version 2.0.0 of rmangal was approved by rOpenSci, four weeks later it made it to CRAN. Following-up on our experience we detail below the reasons why we wrote rmangal, why we submitted our package to rOpenSci and how the peer review improved our package.

Mangal, a database for ecological networks

Ecological networks are defined as a set of species populations (the nodes of the network) connected through ecological interactions (the edges). Interactions are ecological processes in which one species affects another. Although predation is probably the most known and documented interaction, other less noticeable associations are just as essential to ecosystem functioning. For instance, a mammal that unintentionally disperses viable seeds attached to its fur might help plants to thrive. All of these interactions occur simultaneously, shaping ecosystem functioning and making them as complex as they are fascinating.

2 Months in 2 Minutes - rOpenSci News, October 2019

Thu, 17 Oct 2019 00:00:00 +0000

rOpenSci HQ

What would you like to hear about in an rOpenSci Community Call? We are soliciting your “votes” and new ideas for Community Call topics and speakers. Find out how you can influence us by checking out our new Community Calls repository.
Videos, speaker’s slides, resources and collaborative notes from our Community Call on Reproducible Workflows at Scale with drake are posted.
Help wanted! We encourage rOpenSci package authors to help us help you get more contributors to your package. If you label an issue “help wanted” (no hyphen or emojis), those issues can be found in a search of the rOpenSci organization.

What are Your Use Cases for rOpenSci Tools and Resources?

Tue, 15 Oct 2019 00:00:00 +0000

We want to know how you use rOpenSci packages and resources so we can give them, their developers, and your examples more visibility.

It’s valuable to both users and developers of a package to see how it has been used “in the wild”. This goes a long way to encouraging people to keep up development knowing there are others who appreciate and build on their work. This also helps people imagine how they might use a package to address their research question, and provides some code to give them a head-start.

cran checks API: an update

Wed, 09 Oct 2019 00:00:00 +0000

If you have an R package on CRAN, you probably know about CRAN checks. Each package on CRAN, that is not archived on CRAN¹, has a checks page, like this one for ropenaq: https://cloud.r-project.org/web/checks/check_results_ropenaq.html

The table above is results of running R CMD CHECK on the package on a combination of different operating systems, R versions and compilers. CRAN maintainers presumably use these as a basis for getting in touch with maintainers when these checks are failing.

rOpenSci Dev Guide 0.3.0: Updates

Tue, 08 Oct 2019 00:00:00 +0000

As announced in February, we now have an online book containing all things related to rOpenSci software review. Our goal is to update it approximately quarterly - it’s time to present the third version. You can read the changelog or this blog post to find out what’s new in our dev guide 0.3.0!

Updates to our policies and guidance

Scope

We’ve introduced an important change for anyone thinking of submitting a package. We ask authors to select a category in our Aims and Scope under which to submit. We found that the “reproducibility” category was confusing, as almost any R package can be related to reproducibility. We split “reproducibility” into four new categories that fit the narrower topics it previously included. They are:

Academic CV using {vitae}, {scholar} to pull papers, and {tic} for building on Travis.

Thu, 03 Oct 2019 00:00:00 +0000

Package or resource used*

{vitae} and {tic} - both rOpenSci Labs (and excellent).

URL or code snippet for your use case*

Code: https://github.com/seabbs/cv

Image

Link: https://samabbott.co.uk/cv/cv.pdf

Sector

Academic

Field(s) of application

Anything requiring a CV with publications.

What did you do?

Academic CV built using R - updated automatically from Google Scholar each week. See here for the full rendered CV. All other data stored as .csv’s so can be updated on GitHub without touching the code or main document.

Can {drake} RAP? Promoting {drake} for pipeline management in UK government

Wed, 02 Oct 2019 00:00:00 +0000

Package or resource used

URL or code snippet for your use case*

Image

Sector

Government

Field(s) of application

National statistics publications

drake use case involving fires!

Fri, 27 Sep 2019 00:00:00 +0000

rOpenSci package or resource used*

https://gist.github.com/arvi1000/13eda3ad39ed89e9e196c720864b25af

What did you do?

About

This pipeline uses drake to pull tweets from the Twitter API and extract info on where fires are happening in New York City. It illustrates drake’s “what gets done stays done” motto.

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

Fri, 27 Sep 2019 00:00:00 +0000

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.

Magick 2.2

The magick package is one of the most powerful packages for image processing in R. It interfaces to the ImageMagick C++ API and can takes advantage of several other R packages providing imaging functionality in R. Version 2.1 and 2.2 include a lot of small fixes and new features: the NEWS file has the full list of changes.

Reproducible workflows at scale with drake

Tue, 24 Sep 2019 00:00:00 +0000

NA

citecorp: working with open citations

Tue, 17 Sep 2019 00:00:00 +0000

citecorp is a new (hit CRAN in late August) R package for working with data from the OpenCitations Corpus (OCC). OpenCitations, run by David Shotton and Silvio Peroni, houses the OCC, an open repository of scholarly citation data under the very open CC0 license. The I4OC (Initiative for Open Citations) is a collaboration between many parties, with the aim of promoting “unrestricted availability of scholarly citation data”. Citation data is available through Crossref, and available in R via our packages rcrossref, fulltext and crminer. Citation data is also available via the OCC; and this OCC data is now available in R through the new package citecorp.

Use rnaturalearth to get a background map in sf format for plotting with ggplot

Tue, 10 Sep 2019 00:00:00 +0000

Sometimes you just need some points on map. You have lat/lon points, where are you going to get a nice background map that you can plot in R, using ggplot2 and geom_sf? R natural earth!

Package or resource used*

rnaturalearth

URL or code snippet for your use case*

Image

Field(s) of application

e.g. data visualization

What did you do?

Plotted some points on a basemap, applied a map projection

Converting MedDRA Terminology to Linked Data using rdflib

Fri, 06 Sep 2019 00:00:00 +0000

As part of the PhUSE project Going Translational with Linked Data (GoTWLD) we use the rdflib package to translate MedDRA terminology to Linked Data as RDF Triples.

rOpenSci package or resource used*

rdflib

Use Case URL

MedDRA Terminology Conversion to RDF

Image

Sector

Pharmaceutical, Biotech, Medical/Healthcare

Field(s) of application

Medical terminology coding including Adverse Events. Biomedical research, Pharmaceutical industry.

What did you do?

Used an ontology-based approach to convert the multiple hierarchical ASCii files to a unified Linked Data Graph representation. MedDRA terminology files are under license, but the conversion R scripts are freely available to anyone who wishes to convert their MedDRA coding to Linked Data.

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

Fri, 06 Sep 2019 00:00:00 +0000

The UCSC Xena platform provides an unprecedented resource for public omics data from big projects like The Cancer Genome Atlas (TCGA), however, it is hard for users to incorporate multiple datasets or data types, integrate the selected data with popular analysis tools or homebrewed code, and reproduce analysis procedures. To address this issue, we developed an R package UCSCXenaTools for enabling data retrieval, analysis integration and reproducible research for omics data from the UCSC Xena platform¹.

Using pdftools, tabulizer, and writexl to simplify business information handling workflow

Tue, 27 Aug 2019 00:00:00 +0000

Providing a script for a workflow to liberate the contents of PDFs

Packages used

pdftools, tabulizer, writexl

Code Snippet

They have a script which, when they hit the source button, opens a select file dialog box and they pick the pdf, then it saves a word document with the full text, and an excel file of one sheet per table, in the same directory. they also have the option of coming on some R courses I regularly run if they want to start working with the information inside of R.

Using rOpenSci Software Peer Review Guidelines for Teaching

Tue, 27 Aug 2019 00:00:00 +0000

Teaching collaborative software development

In the University of British Columbia’s Master of Data Science program one of the courses we teach is called Collaborative Software Development, DSCI 524. In this course we focus on teaching how to exploit practices from collaborative software development techniques in data scientific workflows. This includes appropriate use of the software life cycle, unit testing and continuous integration, as well as packaging code for use by others.

Introducing Open Forensic Science in R

Tue, 20 Aug 2019 00:00:00 +0000

The free online book Open Forensic Science in R was created to foster open science practices in the forensic science community. It is comprised of eight chapters: an introduction and seven chapters covering different areas of forensic science: the validation of DNA interpretation systems, firearms analysis of bullets and casings, latent fingerprints, shoe outsole impressions, trace glass evidence, and decision-making in forensic identification tasks. The chapters of Open Forensic Science in R have the same five sections: Introduction, Data, R Package(s), Drawing Conclusions, and Case Study. There is R code throughout the chapter to guide the reader along in an analysis, and the case study walks the reader through solving a forensic science problem in R, from reading the data to answering a specific question such as, “Were these two bullets fired by the same gun?”

Using rorcid to generate a website CV

Tue, 20 Aug 2019 00:00:00 +0000

I use rOpenSci’s rorcid package to generate my CV for my academic website. Prior to building the website, I run a script with rorcid that downloads my publications, education, and work history, combines them with some additional annotation data, and saves them as YAML files. These are used by the Hugo site generator to generate my CV.

Package or resource used*

rorcid: https://github.com/ropensci/rorcid

URL or code snippet for your use case

https://www.noamross.net/vitae/

2 Months in 2 Minutes - rOpenSci News, August 2019

Thu, 15 Aug 2019 00:00:00 +0000

rOpenSci HQ

rOpenSci received a $678K award from the Sloan Foundation to expand Software Peer Review.
We are hiring for a new position in statistical software testing and peer review.
Join our next Community Call on Reproducible Workflows at Scale with drake September 24th.
Videos, speakers’ slides, resources and collaborative notes from our Community Calls on Involving Multilingual Communities and Reproducible Research with R are posted.

Software Peer Review

5 community-contributed packages passed software peer review.

Synthesizing population time-series data from the USA Long Term Ecological Research Network

Tue, 13 Aug 2019 00:00:00 +0000

Introduction

The availability of large quantities of freely available data is revolutionizing the world of ecological research. Open data maximizes the opportunities to perform comparative analyses and meta-analyses. Such synthesis efforts will increasingly exploit “population data”, which we define here as time series of population abundance. Such population data plays a central role in testing ecological theory and guiding management decisions. One of the richest sources of open access population data is the USA Long Term Ecological Research (LTER) Network. However, LTER data presents the drawback common to all ecological time-series: extreme heterogeneity derived from differences in sampling designs. We experienced this heterogeneity first hand, upon embarking on our own comparative analysis of population data. Specifically, we noticed that heterogeneities in sampling design made datasets hard to compare, and therefore hard to search and analyze.

Community Call - Reproducible Workflows at Scale with drake

Thu, 08 Aug 2019 00:00:00 +0000

Ambitious workflows in R, such as machine learning analyses, can be difficult to manage. A single round of computation can take several hours to complete, and routine updates to the code and data tend to invalidate hard-earned results. You can enhance the maintainability, hygiene, speed, scale, and reproducibility of such projects with the drake R package. drake resolves the dependency structure of your analysis pipeline, skips tasks that are already up to date, executes the rest with optional distributed computing, and organizes the output so you rarely have to think about data files. This talk demonstrates how to create and maintain a realistic machine learning project using drake-powered automation.

Use of R package review guidelines in independent manuscript review

Thu, 08 Aug 2019 00:00:00 +0000

Package or resource used

rOpenSci package development guide book

URL or code snippet for your use case

https://ropensci.org/blog/2019/04/18/wild-standards/

Image

Sector

academic

Field(s) of application

academic manuscript review

What did you do?

Quoted from Hao Ye @hye in the blog post:

When I was asked to review the code for the pavo 2.0 manuscript1, I had an initial moment of panic – I had no experience doing formal code review. Luckily, I knew that rOpenSci had a set of reviewing guidelines, and that a few MEE Applications papers had used them. The same guidelines are also used by the Journal of Open Source Software (JOSS). Although this submission wasn’t flagged for rOpenSci review, I didn’t see a conflict with using their guidelines for my task.

Teaching how to create high quality R packages

Mon, 05 Aug 2019 00:00:00 +0000

Package or resource used*

rOpenSci package development guide book

URL or code snippet for your use case*

https://github.com/UBC-MDS/DSCI_524_collab-sw-dev

Sector

academic

Field(s) of application

Data Science

What did you do?

the University of British Columbia’s Master of Data Science program one of the courses we teach is called DSCI 524 Collaborative Software Development. In this course, students have to work in teams of 3-4 to create a R package (among other things). One of the resources we recommend the students use for this is the rOpenSci Packages: Development, Maintenance, and Peer Review guide. In particular, we encourage the students to go through the Review template in the appendix of that guide before they hand in their R package for final grading. Instructors and Teaching Assistants for this course also use this Review template to help give both formative feedback and guide summative assessment.

Reproducible Research with R

Tue, 30 Jul 2019 00:00:00 +0000

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

Thu, 18 Jul 2019 00:00:00 +0000

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.

We are seeking a creative, dedicated, and collaborative software research scientist to support a two-year project in launching a new software peer-review initiative. The software research scientist will work on the Sloan Foundation supported rOpenSci project, with rOpenSci staff and a statistical methods editorial board. They will research and develop standards and review guidelines for statistical software, publish findings, and develop R software to test packages against those standards. The software research scientist will work with staff and the board to collaborate broadly with the statistical and software communities to gather input, refine and promote the standards, and recruit editors and peer reviewers. The candidate must be self-motivated, proactive, collaborative and comfortable working openly and reproducibly with a broad online community.

Promoting R and rOpenSci packages in UK local government

Wed, 17 Jul 2019 00:00:00 +0000

rOpenSci package or resource used*

ropenaq

Description

Trafford Council’s Trafford Data Lab are publishing #rstats recipes for local government colleagues. The aim of the project is to embed an analytical workflow across UK local government that encourages openness, reproducibility and collaboration by promoting the use of R. We’ve used and plan to use a number of rOpenSci packages in the recipes including ropenaq and fingertipsR. These particular packages provide an intuitive way of retrieving open data within R without the need to familiarise yourself with often complex APIs.

Querying linked data to improve public services

Wed, 17 Jul 2019 00:00:00 +0000

Package used

ghql

URL or code snippet for your use case

What did you do?

The ghql package was used to retrieve open data held in a triple store that was queryable with CubiQL, a GraphQL service. The data was visualised in a Shiny application that formed part of a suite of apps used in the Trafford Workless Pilot. The pilot was part of the EU funded Horizon 2020 OpenGovIntelligence project that used linked data to improve public services.

Using fingertipsR for public health data in UK local government

Wed, 17 Jul 2019 00:00:00 +0000

Package used

fingertipsR by Sebastian Fox

URL or code snippet for your use case

Image

Sector

government

Field(s) of application

public health

Aggregating spatial data with the grainchanger package

Tue, 16 Jul 2019 00:00:00 +0000

The grainchanger package provides functionality for data aggregation to a coarser resolution via moving-window or direct methods.

Why do we need new methods for data aggregation?

As landscape ecologists and macroecologists, we often need to aggregate data in order to harmonise datasets. In doing so, we often lose a lot of information about the spatial structure and environmental heterogeneity of data measured at finer resolution.

The issues around scale disconnects are both conceptual and practical:

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

Mon, 15 Jul 2019 00:00:00 +0000

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 & Computational Research program, will be used to expand our efforts in software peer review.

Software peer review has become a core part of rOpenSci, helping improve scientific software quality, drive best engineering practices into scientific communities, and building community and collaboration through open, constructive reviews. We’re excited to expand our work in this important area. Here’s what we’ll be doing in the next two years with this support:

Community Call - Reproducible Research with R

Thu, 11 Jul 2019 00:00:00 +0000

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

From Karthik Ram you will learn about holepunch, an R package that will take any GitHub repo with R scripts and R markdown files and quickly turn it in into a free, live RStudio server where anyone can run your code!

Chat with rOpenSci Contributors at useR!2019

Mon, 08 Jul 2019 00:00:00 +0000

Three members of the rOpenSci team - Scott Chamberlain, Jenny Bryan, and Rich FitzJohn - as well as many community members will give talks at useR!2019. Many other package authors, maintainers, reviewers and unconf participants will be there too. Don’t hesitate to ask them about rOpenSci packages, software peer review, community, or just say hello if you’re looking for a friendly face.

We’ve listed their talks for you. Search the schedule for details.

Wednesday, July 10

Julia Stewart Lowndes Keynote! R for better science in less time

Using bomrang to correlate weather conditions to sorghum stalk rot (charcoal rot)

Mon, 01 Jul 2019 00:00:00 +0000

Package or resource used

bomrang

URL or code snippet for your use case

Full article: https://communities.grdc.com.au/field-crop-diseases/sorghum-disease-survey/

Code gist: https://gist.github.com/adamhsparks/23d6266f4a2b5f19f9edef6970f0364a

Image

Sector

academic

Field(s) of application

botanical epidemiology, plant pathology, agronomy

What did you do?

I used bomrang’s get_historical() to fetch weather data, rainfall and temperature, for four stations in Queensland and New South Wales to create a climogram to illustrate how rainfall seemingly affected the distribution of sorghum charcoal rot (Macrophomina phaseolina) during the summer season of 2018/19. The article was published online as a part of the GRDC Communities Field Crops Diseases blog.

Involving Multilingual Communities

Fri, 28 Jun 2019 00:00:00 +0000

2 Months in 2 Minutes - rOpenSci News, June 2019

Thu, 20 Jun 2019 00:00:00 +0000

rOpenSci HQ 👨🏽‍💻👩🏼‍💻 🏗️

Join our next Community Call on Involving Multilingual Communities June 28th.
Video of our Community Call on Security for R is up, with a long list of resources.
Our Community Manager, Stefanie Butland, spoke at R-Ladies Seattle and Fred Hutch about rOpenSci, Learning R, and Building Community May 22nd.

Software Peer Review ✔

6 community-contributed packages passed software peer review

nbaR - R Package Client for the Netherlands Biodiversity API
- Author: Hannes Hettling
- Issue: ropensci/onboarding#257
- Reviewers:
  - Dom Bennett
  - Max Joseph
git2rdata - Store and Retrieve Data.frames in a Git Repository
- Author: Thierry Onkelinx
- Issue: ropensci/onboarding#263
- Reviewers:
  - Jenny Bryan
  - Brodie Gaslam
citesdb - A high-performance database of shipment-level CITES trade data
- Author: Noam Ross
- Issue: ropensci/onboarding#292
- Reviewers:
  - pachamaltese
  - Xavier Rotllan-Puig
MtreeRing - A Shiny Application for Automatic Measurements of Tree-Ring Widths on Digital Images
- Author: Jingning Shi
- Issue: ropensci/onboarding#287
- Reviewers:
  - Brandon Hurr
  - Rory Nolan
rromeo - An R Client for SHERPA/RoMEO API
- Author: Matthias Grenié
- Issue: ropensci/onboarding#285
- Reviewers:
  - Philipp Ottolinger
  - Bruna Wundervald
tidync - A Tidy Approach to ‘NetCDF’ Data Exploration and Extraction
- Author: Michael Sumner
- Issue: ropensci/onboarding#174
- Reviewers:
  - Tim Lucas
  - Jakub Nowosad

Consider submitting your package or volunteering to review.

Community Call - Involving Multilingual Communities

Thu, 13 Jun 2019 00:00:00 +0000

rOpenSci’s community is increasingly international and multilingual. While we have operated primarily in English, we now receive submissions of packages from authors whose primary language is not. As we expand our community in this way, we want to learn from the experience of other organizations. How can we manage our peer-review process and open-source projects to be welcoming to non-native English speakers?

Our guest speakers will include:

Rayna Harris, who has co-led work with The Carpentries in internationalization of curricula.
Emilio Bruna, who as editor-in-chief of Biotropica, manages a journal with a heavily tropical-country audience and authorship base.

The call will be moderated by Melina Vidoni, an associate editor for rOpenSci software peer review. There will be 20 minutes for Q & A following the presentations.

Taking over maintenance of a software package

Wed, 12 Jun 2019 00:00:00 +0000

Software is maintained by people. While software can in theory live on indefinitely, to do so requires people. People change jobs, move locations, retire, and unfortunately die sometimes. When a software maintainer can no longer maintain a package, what happens to the software?

Because of the fragility of people in software, in an ideal world a piece of software should have as many maintainers as possible. Increasing maintainers increases the so-called bus factor. A lower number of maintainers means fewer people have to get hit by a bus to then have no maintainers.

Introducing the new rOpenSci docs server

Fri, 07 Jun 2019 00:00:00 +0000

As part of our continuous effort to improve rOpenSci infrastructure, we are rolling out a new service to automatically build and host documentation for all rOpenSci packages.

The webpages are generated using the popular pkgdown system with our rOpenSci template, and get automatically published on https://docs.ropensci.org/. Some examples:

We intend this to become the central place to find documentation for rOpenSci packages. We are still rolling this out so not all packages are there yet, but the majority is online now.

get_clean_obs R Function (searching, pulling and cleaning citizen science records from iNaturalist and GBIF)

Thu, 06 Jun 2019 00:00:00 +0000

An R function that leverages the rgbif and spocc packages to search for, pull down, combine and clean records of a single species (with lat/lon bounding boxes). A continuing work in progress, but hopefully useful for folks interested in pulling records from these sources. It also has some (slow, but tricky) work arounds when querying large numbers (up to 200k) from these sources.

Package or resource used*

spocc, rgbif

URL or code snippet for your use case*

https://github.com/keatonwilson/insect_migration/blob/ec66ff976155fd75982dce0ebf42644077127b53/scripts/get_clean_obs_function.R

Access Publisher Copyright & Self-Archiving Policies via the 'SHERPA/RoMEO' API

Tue, 04 Jun 2019 00:00:00 +0000

We’ve been following rOpenSci’s work for a long time, and we use several packages on a daily basis for our scientific projects, especially taxize to clean species names, rredlist to extract species IUCN statuses or [treeio](many probs with this post) to work with phylogenetic trees. rOpensci is a perfect incarnation of a vibrant and diverse community where people learn and develop new ideas, especially regarding scientific packages. We’ve also noticed how much the thorough review process improves the quality of the packages that join the rOpenSci ecosystem. And while we were admiring the dynamics of rOpenSci community, we started to wonder how we could contribute to this ecosystem. And this is how we started our quest to find a project that could fit rOpenSci goals while at the same time teach us new skills.

osmdata use case: Bicycle network analysis of Auckland

Thu, 30 May 2019 00:00:00 +0000

Package or resource used*

osmdata

URL or code snippet for your use case*

Spatial Bike Network Analysis in Auckland

Sector

Other

Field(s) of application

transport and planning

What did you do?

I used the osmdata package to retrieve and analyse Open Street Map (OSM) bike data given the flurry of bike route construction in Auckland. I also compared to the bike counter data provided by Auckland Transport to visualise our bike networks.

Using bib2df to parse the R Journal archives

Wed, 29 May 2019 00:00:00 +0000

Package or resource used*

bib2df

URL or code snippet for your use case*

https://blog.r-hub.io/2019/05/29/keep-up-with-cran/

journal <- bib2df::bib2df("https://journal.r-project.org/archive/RJournal.bib")
knitr::kable(
 journal[grepl("CRAN", journal$TITLE), c("TITLE", "MONTH", "YEAR", "URL")]
)

Sector

other

Field(s) of application

R package development

What did you do?

I used bib2df to parse the bibliography file containing information about all previous articles of the R Journal, to then filter articles whose title contained the word “CRAN”, since I wanted to see how often the CRAN team had published articles giving updates on their policies and processes.

ramlegacy: a package for RAM Legacy Database

Tue, 28 May 2019 00:00:00 +0000

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. The package accomplishes all this by:

Providing a function download_ramlegacy(), to download all the available versions of the RAM Database and cache them on the user’s computer in a location provided by the rappdirs package. This way once a version has been downloaded it doesn’t need to be re-downloaded for subsequent analysis.
Supporting reading in specified tables or all tables from a cached version of the database through the function load_ramlegacy()
Providing a function ram_dir() to view the path of the rappdirs location where the downloaded database was cached.

The primary motivation behind developing the caching behavior of the package was to save the user time and effort spent in re-downloading different versions of the database as part of any future analysis.

rodev: helpers for rOpenSci package authors

Tue, 21 May 2019 00:00:00 +0000

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.

Inspired by the usethis package, we’ve started work on our specific helpers for rOpenSci package authors, rodev. In this note, we’ll present some of the helpers it contains at the moment, and ask for your feedback as an rOpenSci package author.

rcrossref for #TidyTuesday

Fri, 17 May 2019 00:00:00 +0000

Package or resource used*

rcrossref

URL or code snippet for your use case*

https://twitter.com/jakekaupp/status/1129202271789748234

Sector

Other

Field(s) of application

Bibliometrics

What did you do?

In week 20 of #TidyTuesday, a #rstats community exercise around cleaning and visualizing data, I used rcrossref to get the citation counts for Nobel Prize winners (DOI was present in the dataset) and visualized the citation patterns by author and Nobel category (Chemistry, Physics and Medicine)

rOpenSci Dev Guide 0.2.0: Updates Inside and Out

Thu, 16 May 2019 00:00:00 +0000

As announced in our recent post about updates to our Software Peer Review system, all our package development, review and maintenance is available as an online book. Our goal is to update it approximately quarterly so it’s already time to present its second official version! You can read the changelog or this blog post to find out what’s new in our dev guide 0.2.0!

A more legit and accessible book

Let’s start with very exciting news, the dev guide now has a cover, designed by Oz Locke from Locke Creatives!

POWER to the People

Tue, 14 May 2019 00:00:00 +0000

NASA generates and provides heaps of data to the scientific community. Not all of it is looking out at the stars. Some of it is looking back at us here on Earth. NASA’s Earth science program observes, understands and models the Earth system¹. We can use these data to discover how our Earth is changing, to better predict change, and to understand the consequences for life on Earth.

The Earth science program includes the Prediction of Worldwide Energy Resource (POWER) project, which was initiated to improve upon the current renewable energy data set and to create new data sets from new satellite systems. The POWER project targets three user communities: 1) Renewable Energy (SSE), 2) Sustainable Buildings (SB) and 3) Agroclimatology (AG)¹ and covers 140+ different parameters.

Can rainfall be a useful predictor of epidemic risk across temporal and...

Fri, 10 May 2019 00:00:00 +0000

rOpenSci package or resource used*

nasapower

URL

https://speakerdeck.com/emdelponte/can-rainfall-be-a-useful-predictor-of-epidemic-risk-across-temporal-and-spatial-scales?slide=23

Sector

Academic

Field(s) of application

Plant disease epidemiology, risk mapping, rainfall monitoring

What did you do?

I used the package, with the help of its maintainer @adamhsparks, to download rainfall data for specific time periods matching the pre- and early-season of period of soybean growth in Brazil. It will be further used to explore associations between rainfall and patterns of dispersal of a fungal disease of soybean over large region across years.

Open Trade Statistics

Thu, 09 May 2019 00:00:00 +0000

Introduction

Open Trade Statistics (OTS) was created with the intention to lower the barrier to working with international economic trade data. It includes a public API, a dashboard, and an R package for data retrieval.

The project started when I was affected by the fact that many Latin American Universities have limited or no access to the United Nations Commodity Trade Statistics Database (UN COMTRADE).

There are alternatives to COMTRADE, for example the Base Pour L’Analyse du Commerce International (BACI) constitutes an improvement over COMTRADE as it is constructed using the raw data and a method that reconciles the declarations of the exporter and the importer. The main problem with BACI is that you need UN COMTRADE institutional access to download their datasets.

Security for R

Tue, 07 May 2019 00:00:00 +0000

Using drake to power a new soil respiration database

Sat, 04 May 2019 00:00:00 +0000

Package or resource used*

https://github.com/bpbond/cosore/blob/6b96bf9afbc3cb8e995c4b1e65b7c6af78bdc82f/README.md

URL or code snippet for your use case*

Image

Sector

Academic

Field(s) of application

Earth sciences, climate change, ecology

What did you do?

Earth system scientists increasingly use online data repositories to store, synthesize, and perform meta-analyses of e.g. forest growth, plant characteristics, and land-atmosphere energy fluxes (see for example Ameriflux). No such database exists for continuous soil respiration, the land-to-atmosphere CO2 flux measured continuously by automated systems around the world, however. This is the gap my nascent cosore package aims to fill. drake provides the infrastructure for tracking out-of-date soil respiration datasets contributed by authors; efficiently rebuilding them into a single, standardized form; and verifying reproducibility.

qualtRics: the Stack Overflow Developer Survey

Wed, 01 May 2019 00:00:00 +0000

rOpenSci package used

qualtRics

Use case

Stack Overflow Developer Survey 2019 results

Image

Sector

industry

Field(s) of application

surveys

What did you do?

As the data scientist who worked on both planning and analyzing Stack Overflow’s annual survey, I used qualtRics to access the almost 90,000 responses to our survey. Using qualtRics made our workflow more reproducible and simpler.

Relaunching the qualtRics package

Tue, 30 Apr 2019 00:00:00 +0000

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. 😎

Qualtrics is an online survey and data collection software platform. Qualtrics is used across many domains in both academia and industry for online surveys and research, including by me at my day job as a data scientist at Stack Overflow. While users can manually download survey responses from Qualtrics through a browser, importing this data into R is then cumbersome. The qualtRics R package implements the retrieval of survey data using the Qualtrics API and aims to reduce the pre-processing steps needed in analyzing such surveys. This package has been a huge help to me in my real day-to-day work, and I have been so grateful for the excellent work of the package’s original authors, including the previous maintainer Jasper Ginn. This package is currently the only package on CRAN that offers functionality like this for Qualtrics’ API, and is included in the official Qualtrics API documentation.

conditionz: control how many times conditions are thrown

Wed, 24 Apr 2019 00:00:00 +0000

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

This package arises from an annoyance in another set of packages I maintain: The brranching package uses the taxize package internally, calling it’s function taxize::tax_name(). The taxize::tax_name() function throws useful messages to the user if their API key is not found, and gives them instructions on how to find it. However, the user does not have to get an API key. If they don’t they then get subjected to lots of repeats of the same message.

Join, split, and compress PDF files with pdftools

Wed, 24 Apr 2019 00:00:00 +0000

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

Split and Join PDF files

It is now possible to split, join, and compress pdf files with pdftools. For example the pdf_subset() function creates a new pdf file with a selection of the pages from the input file:

When Standards Go Wild - Software Review for a Manuscript

Thu, 18 Apr 2019 00:00:00 +0000

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.

I was surprised and intrigued to see an example of our software peer review guidelines being used in a manuscript review, independent of our formal collaboration with the journal Methods in Ecology and Evolution (MEE). This is exactly the kind of thing rOpenSci is working to enable by developing a good set of practices that broadly apply to research software.

Get tweet status ID from CrossRef Event Data with crevents

Fri, 12 Apr 2019 00:00:00 +0000

Package or resource used

crevents

URL or code snippet for your use case

https://github.com/tts/aaltoced/blob/b617ec401473cfe7928723e8f2d68be8fa4945ea/getdata.R#L36-L45

Sector

Academic

Field(s) of application

Bibliometrics, altmetrics

What did you do?

I built a Shiny web app on those recent publications of our university that have been tweeted by their DOI. For this, I first queried CrossRef Event Data with crevents, extracted the tweet status id’s from the result, and then fetched the tweet text and other info with rtweet. For the whole story, see my blog post.

Community Call - Security for R

Tue, 09 Apr 2019 00:00:00 +0000

“Security” can be a daunting, scary, and (frankly) quite often a very boring topic. BUT!, we promise that this Community Call on May 7th will be informative, engaging, and enlightening (or, at least not boring)!

Applying security best practices is essential not only for developers or sensitive data storage but also for the everyday R user installing R packages, contributing to open source, working with APIs or remote servers. However, keeping up-to-date with security best practices and applying them meticulously requires significant effort and is difficult without expert knowledge. On this Call you’ll hear about how the ropsec package can help you and you’ll learn the inner secrets of maintaining confidentiality, integrity, and availability throughout all your data science workflows.

Getting your toes wet in R: Hydrology, meteorology, and more

Tue, 02 Apr 2019 00:00:00 +0000

Importance of Hydrology

Given that liquid water is essential to life on Earth, water research cuts across numerous disciplines including hydrology, meteorology, geography, climate science, engineering, ecology, and more. Numerous R packages have emerged from this diversity of approaches, and we recently gathered many of them into a new rOpenSci task view which we broadly titled ‘Hydrology’ and published to CRAN. Our intent is to be exhaustive and compile R packages to access, model, and summarise information related to the movement of water across the Earth’s landscape. We hope to contribute to a nascent community of hydrological R users and develop an infrastructure of packages that provide a comprehensive toolkit for water practitioners who use R as their preferred computational analysis tool. Making sense of water data is critical to understanding the response of landscapes to a changing climate. Consolidating water-related packages will promote their usage and discovery and ultimately facilitate reproducible workflows for water research. Since this is a new task view, it serves our purpose to evaluate the current State of Hydrology in R and look at the interdependency of hydrology packages relative to some better known collections of packages in the general R ecosystem.

rgbif: get a little or a lot of occurrence data

Tue, 02 Apr 2019 00:00:00 +0000

This use case was presented by Kathryn Turner as part of a Community Call on Research Applications of rOpenSci Taxonomy and Biodiversity Tools

Package or resource used*

rgbif

URL or code snippet for your use case*

Code example to download occurrence data from GBIF for a handful of species, and scaling up to several thousand

Paper: “Occurrence data tells us about abiotic tolerances”

Field(s) of application

ecology

Rencontre scientifique, URFIST de Bordeaux

Fri, 29 Mar 2019 14:40:00 +0000

Our software engineer and associate editor Maëlle Salmon will give an invited talk about rOpenSci Software Peer Review, in French, at the “Repenser la robustesse et la fiabilité en recherche : les chercheurs face à la crise de la reproductibilité” scientific meeting organized by URFIST de Bordeaux.

taxize: Understanding how seafood mislabelling misrepresents the conservation status of the fish on your plate

Fri, 29 Mar 2019 00:00:00 +0000

This use case was presented by Margaret Siple as part of a Community Call on Research Applications of rOpenSci Taxonomy and Biodiversity Tools

Package used

taxize

Links to use case

Code example: Given genus names, retrieve family names and Given a list of species names, get their IUCN status
Paper: Financial and Ecological Implications of Global Seafood Mislabeling

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rBiodiversidata

Thu, 28 Mar 2019 00:00:00 +0000

This are scripts used for the Biodiversidata Project that are useful for:

Retrieving Conservation Status and Population Trend (IUCN).
Checking Species Names.
Retrieving Taxonomic Information for a Species.

Package or resource used

rredlist, taxize

URL or code snippet for your use case*

https://github.com/bienflorencia/rBiodiversidata

Sector

University of Lincoln, UK

Field(s) of application

ecology, conservation

Research Applications of rOpenSci Taxonomy and Biodiversity Tools

Wed, 27 Mar 2019 00:00:00 +0000

weathercan: Exploring extreme weather events in my neighbourhood

Wed, 27 Mar 2019 00:00:00 +0000

rOpenSci Package used