Publications by rOpenSci - open tools for open science
What birds are observed near Radolfzell? Bird occurrence data in R
Thanks to the first post of the series we know where to observe birds near Radolfzell’s Max Planck Institute for Ornithology, so we could go and do that! Or we can stay behind our laptops and take advantage of eBird, a fantastic bird sightings aggregator! As explained by Matt Strimas-Mackey in his recent blog post, “The eBird database current...
9078 sym R (6700 sym/13 pcs) 10 img 2 tbl
rgbif: seven years of GBIF in R
rgbif was seven years old yesterday! What is rgbif? rgbif gives you access to data from the Global Biodiversity Information Facility (GBIF) via their API. A samping of use cases covered in rgbif: Search for datasets Get metrics on usage of datasets Get metadata about organizations providing data to GBIF Search taxonomic names Get quick taxonomi...
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What’s this bird? Classify old natural history drawings with R
In this new post, we’re taking a break from modern birding data in our birder’s series… let’s explore gorgeous drawings from a natural history collection! Armed with rOpenSci’s packages binding powerful C++ libraries and open taxonomy data, how much information can we automatically extract from images? Maybe not much, but we’ll at lea...
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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 characte...
8486 sym R (10278 sym/14 pcs) 6 img 1 tbl
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, t...
5646 sym R (3896 sym/7 pcs) 3 tbl
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. c...
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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 ...
9010 sym R (5600 sym/15 pcs) 6 img
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 ou...
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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 reproducible res...
814 sym 1 tbl
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 moistu...
9368 sym R (12042 sym/28 pcs) 28 img