UPDATE: there were some errors in the tests for taxize, so the binaries aren’t avaiable yet. You can install from source though, see below. Getting taxonomic information for the set of species you are studying can be a pain in the ass. You have to manually type, or paste in, your species one-by-one. Or, if you are lucky, there is a web service in which you can upload a list of species....
Note: This post is cross-posted on Sandra Chung’s blog here. The rise of the unconference The Ecological Society of America meeting is holding its 98th annual meeting next year in Minneapolis, MN. Several thousand students and professionals in ecological science and education will gather to hear and read the latest work and ideas in ecology in the familiar poster and lecture formats that are the core of every major scientific conference....
It can be a pain in the ass to get taxonomic names. For example, I sometimes need to get all the Class names for a set of species. This is a relatively easy problem using the ITIS API (example below). The much harder problem is getting all the taxonomic names downstream. ITIS doesn’t provide an API method for this - well, they do (getHirerachyDownFromTSN), but it only provides direct children (e....
UPDATE: In response to Jarrett’s query I laid out a separate use case in which you may want to query by higher taxonomic rankings than species. See below. In addition, added examples of querying by location in reply to comments by seminym. We have been working on an R package to get GBIF data from R, with the stable version available through CRAN, and the development version available on GitHub at https://github....
We (rOpenSci) started a repo to wrap the API for VertNet, an open access online database of vertebrate specimen records across many collection holders. Find the open source code here - please contribute if you are so inclined. We had a great Google Summer of Code student, Vijay Barve contributing to the repo this summer, so it is getting close to being CRAN-able. Most of the functions in the repo get you the raw data, but there were no functions to visualize the data....
Example of using the Global Names Resolver API to check species names There are a number of options for resolution of taxonomic names. The Taxonomic Name Resolution Service (TNRS) comes to mind. There is a new service for taxonomic name resoultion called the Global Names Resolver. They describe the service thusly “Resolve lists of scientific names against known sources. This service parses incoming names, executes exact or fuzzy matching as required, and displays a confidence score for each match along with its identifier....
So the Weecology folks have published a large dataset on mammal communities in a data paper in Ecology. I know nothing about mammal communities, but that doesn’t mean one can’t play with the data… Their dataset consists of five csv files: communities, references, sites, species, and trapping data Where are these sites, and by the way, do they vary much in altitude? Let’s zoom in on just the states What phylogenies can we get for the species in this dataset?...
I am part of the rOpenSci development team (along with Carl Boettiger, Karthik Ram, and Nick Fabina). Our website: http://ropensci.org/. Code at Github: https://github.com/ropensci We entered two of our R packages for integrating with PLoS Journals (rplos) and Mendeley (RMendeley) in the Mendeley-PLoS Binary Battle. Get them at GitHub (rplos; RMendeley). These two packages allow users (from R! of course) to search and retrieve data from PLoS journals (including their altmetrics data), and from Mendeley....
The team at rOpenSci and I have been working on a wrapper for the USA National Phenology Network API. The following is a demo of some of the current possibilities. We will have more functions down the road. Get the publicly available code, and contribute, at Github here. If you try this out look at the Description file for the required R packages to run rnpn. Let us know at Github (here) or at our website http://ropensci....