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

Thanks to the second post of the series where we obtained data fromeBird we knowwhat birds were observed in the county of Constance. Now, not allspecies’ names mean a lot to me, and even if they did, there are a lotof them.

In this new post, we’re taking a break from modern birding data in ourbirder’s series… let’s exploregorgeous drawings from a natural history collection!

taxize was seven years old this last Saturday! What is taxize? taxize is designed around making working with taxonomic names easier - abstracting away the details of what each of 20 or so taxonomic data sources require for a given use case.

What is Taxonomy? Taxonomy in its most general sense is the practice and science of classification. It can refer to many things. You may have heard or used the word taxonomy used to indicate any sort of classification of things, whether it be companies or widgets. Here, we’re talking about biological taxonomy, the science of defining and naming groups of biological organisms.

Programmatic access to biodiversity data is revolutionising large-scale, reproducible biodiversity research. In the marine realm, the largest global database of species occurrence records is the Ocean Biogeographic Information System, OBIS. As of January 2017, OBIS contains 47.78 million occurrences of 117,345 species, all openly available and accessible via the OBIS API.

We just released v0.3 of taxize. For details on the update, see the release notes. Some new features New function iplant_resolve() to do name resolution using the iPlant name resolution service. Note, this is different from http://taxosaurus.org/ that is wrapped in the tnrs() function. New function ipni_search() to search for names in the International Plant Names Index (IPNI). See below for more.

We just released a new version of taxize - version 0.2.0. This release contains a number of new features, and bug fixes. Here is a run down of some of the changes: First, install and load taxize install.packages("rgbif") library(taxize) New things New functions: class2tree Sometimes you just want to have a visual of the taxonomic relationships among taxa.

R has a reputation of not playing nice on the web. At rOpenSci, we write R pacakages to bring data from around the web into R on your local machine - so we mostly don’t do any dev for the web. However, the United States Geological Survey (USGS) recenty held an app competition - it was a good opportunity to play with R on the web. We won best overall app as described in an earlier post on this blog.

The following was a guest post from Ignasi Bartomeus, originally posted on his blog on 26 Nov, 2012. Check out a related blog post here. Note the functionality discussed in this post is now in our taxize package under the function gisd_isinvasive. We hacked out a quick Shiny app so you can play around with the below function in taxize on the web to get invasive status and plot it on a phylogeny. Check it out here.