Blog Archives

pubchunks: extract parts of scholarly XML articles

pubchunks is a package grown out of the fulltext package. fulltext provides a single interface to many sources of full text scholarly articles. As part of the user flow in fulltext there is an extraction step where fulltext::chunks() pulls parts of articles out of XML format article files. As part of making fulltext more maintainable and focused on simply fetching articles, and realizing that...

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Parsing Metadata with R – A Package Story

Parsing Metadata with R – A Package Story

Every R package has its story. Some packages are written by experts, some by novices. Some are developed quickly, others were long in the making. This is the story of jstor, a package which I developed during my time as a student of sociology, working in a research project on the scientific elite within sociology. Writing the package has taught me many things...

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Distinguish yourself in CRAN person() with ORCID

Distinguish yourself in CRAN person() with ORCID

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

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The av Package: Production Quality Video in R

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

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

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

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

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outcomerate: Transparent Communication of Quality in Social Surveys

outcomerate: Transparent Communication of Quality in Social Surveys

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

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tinkr: editing Markdown documents using XML tools

Remember our recent post showing that one can wrangle Markdown files programmatically without regex? That tech note showed how to convert Markdown bodies to XML in order to extract information from them. Now, this post goes one step further and presents tinkr, a package for converting .md and .Rmd files to XML, editing them, and… writing them back as Markdown! General tinkr workflow The goal of tinkr...

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Mapping the 2018 East Africa floods from space with smapr

Mapping the 2018 East Africa floods from space with smapr

Hundreds of thousands of people in east Africa have been displaced and hundreds have died as a result of torrential rains which ended a drought but saturated soils and engorged rivers, resulting in extreme flooding in 2018. This post will explore these events using the R package smapr, which provides access to global satellite-derived soil moisture data collected by the...

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Chat with the rOpenSci team at upcoming meetings

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

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Building Reproducible Data Packages with DataPackageR

Building Reproducible Data Packages with DataPackageR

Sharing data sets for collaboration or publication has always been challenging, but it’s become increasingly problematic as complex and high dimensional data sets have become ubiquitous in the life sciences. Studies are large and time consuming; data collection takes time, data analysis is a moving target, as is the software used to carry it out. In the vaccine space (where...

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