Data

Why Butte County? I went to college at California State University, Chico - in Butte County, CA. I did a BA degree in Biology there. It was a great program as it was heavily focused on natural history - with classes on herps, birds, insects, fish, etc. Specimen collections data Specimen collections data are increasingly being digitized, and often accessed via largeish platforms like GBIF and iDigBio. Here I’ll explore Butte County data found with iDigBio with the spocc R package. You could also use the ridigbio package to go directly to iDigBio data. ...

Measuring use of open source software isn’t always straightforward. The problem is especially acute for software targeted largely at academia, where usage is not measured just by software downloads, but also by citations. Citations are a well-known pain point because the citation graph is privately held by iron doors (e.g., Scopus, Google Scholar). New ventures aim to open up citation data, but of course it’s an immense amount of work, and so does not come quickly. ...

The paper One paper from my graduate work asked most generally ~ “How much does the variation in magnitudes and signs of species interaction outcomes vary?”. More specifically, we wanted to know if variation differed among species interaction classes (mutualism, competition, predation), and among various “gradients” (space, time, etc.). To answer this question, we used a meta-analysis approach (rather than e.g., a field experiment). We published the paper recently. p.s. I really really wish we would have put it in an open access journal… ...

ScienceOnline Climate I recently attended ScienceOnline Climate, a conference in Washington, D.C. at AAAS offices. You may have heard of the ScienceOnline annual meeting in North Carolina - this was one of their topical meetings focused on Climate Change. Another one is coming up in October, ScienceOnline Oceans. Search Twitter for #scioClimate (or the entire list of hashtags here) for tweets from the conference. One of the sessions I attended was focused on how to democratize climate change knowledge, moderated by a fellow from the Union of Concerned Scientists. Search Twitter for #sciodemocracy to see the conversation from that session. There was a lot of very interesting discussion. ...

Have you heard of DataONE? It stands for the Data Observation Network for Earth, and I am involved in the Community Education and Engagement working group at DataONE. We try to communicate about data, data management, and similar things to scientists and other DataONE stakeholders. At our last meeting, we decided to start a blog aggregator to pull in to one place blog posts about data, data management, and related topics. Those reading this blog have likely heard of R-Bloggers - and there are many more aggregator blogs. We are calling this blog aggregator Coffeehouse - as it’s sort of a place to gather to talk/read about ideas. Check it out here. If you blog about data management think about adding your blog to Coffeehouse - go to the Add your blog page to do so. A screenshot: ...

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. Encyclopedia of Life (EOL) has a service where you can do this here. But is this reproducible? No. ...

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. But a subset of these people will get a taste of something a little bit different: an unconference within the 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.g., the genera within a tribe - but it won’t give all the species within each genus). ...

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.com/rgbif ...

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. Since much of the data records of latitude and longitude data, maps are a natural visualization to use. ...