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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 I work) we analyze collections of high-dimensional immunological data sets from a variety of different technologies (RNA sequencing, cytometry, multiplexed antibody binding, and others)....

What have these birds been studied for? Querying science outputs with R

In the second post of the series where we obtained data from eBird we determined what birds were observed in the county of Constance, and we complemented this knowledge with some taxonomic and trait information in the fourth post of the series. Now, we could be curious about the occurrence of these birds in scientific work. In this post, we will query the scientific literature and an open scientific data repository for species names: what have these birds been studied for?...

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

A while ago we onboarded an exciting package, codemetar by Carl Boettiger. codemetar is an R specific information collector and parser for the CodeMeta project. In particular, codemetar can digest metadata about an R package in order to fill the terms recognized by CodeMeta. This means extracting information from DESCRIPTION but also from e.g. continuous integration1 badges in the README! In this note, we’ll take advantage of codemetar::extract_badges function to explore the diversity of badges worn by the READMEs of CRAN packages....

In praise of Commonmark: wrangle (R)Markdown files without regex

You might have read my blog post analyzing the social weather of rOpenSci onboarding, based on a text analysis of GitHub issues. I extracted text out of Markdown-formatted threads with regular expressions. I basically hammered away at the issues using tools I was familiar with until it worked! Now I know there’s a much better and cleaner way, that I’ll present in this note. Read on if you want to extract insights about text, code, links, etc....

What are these birds? Complement occurrence data with taxonomy and traits information

Thanks to the second post of the series where we obtained data from eBird we know what birds were observed in the county of Constance. Now, not all species’ names mean a lot to me, and even if they did, there are a lot of them. In this post, we shall use rOpenSci’s packages accessing taxonomy and trait data in order to summarize some characteristics of the birds’ population of the county: armed with scientific and common names of birds, we have access to plenty of open data!...

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