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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)....
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?...
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!...
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 least have explored image manipulation, optical character recognition (OCR), language detection, taxonomic name resolution with rOpenSci’s packages. Free natural history images and appropriate R tooling!...
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 currently contains over 500 million records of bird sightings, spanning every country and over 98% of species, making it an extremely valuable resource for bird research and conservation....
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