Working on translating a key to the European shield bug nymphs (Puchkov, 1961) I thought I would look for pictures of the earlier life stages (nymphs, Fig. 1) of shield bugs (Pentatomoidea) on iNaturalist and found few observations actually had the life stage annotation.

Last november I wrote a blog post about how to model the taxonomic coverage of identification keys. I wanted to model this coverage to be able to determine to what extent an identification key applies to a given observation or specimen, for use in my Library of Identification Resources project. For the same project I also find it useful to be able to archive identification keys.

The main feature of the Library of Identification Resources is the description of the identification key (or matrix, reference, etc.). This description should on its basis specify when the key can or should be used.

The h-index is a metric that was invented to summarise the publication output and impact of researchers. In a new GigaScience article, authors from the University of New South Wales (Australia) adopt the controversial metric for a completely different purpose: to explore systematic differences in research interest ( taxonomic bias ), using mammals as an example.

Since around this time last year, I have been working on creating a library of identification resources. Here, “identification resources” are identification keys, multi-access (matrix) keys, other works that can aid in the identification of species. The project is managed on GitHub: https://github.com/identification-resources.

I keep returning to the problem of viewing large graphs and trees, which means my hard drive has accumulated lots of failed prototypes. Inspired by some recent discussions on comparing taxonomic classifications I decided to package one of these (wildly incomplete) prototypes up so that I can document the idea and put the code somewhere safe.

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

\ Code is often arranged in packages for any given language. Packages are often cataloged in a package registry of some kind: NPM for node, crates.io for Rust, etc. For R, that registry is either CRAN or Bioconductor (for the most part). CRAN has the concept of an archived package.

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.

taxizedb arose from pain in using taxize when dealing with large amounts of data in a single request or doing a lot of requests of any data size. taxize works with remote data sources on the web, so there’s a number of issues that can slow the response down: internet speed, server response speed (was a response already cached or not; or do they even use caching), etc.