Ecology

Carl Boettiger, a graduate student at UC Davis, just got two packages on CRAN. One is treebase, which which handshakes with the Treebase API. The other is rfishbase, which connects with the Fishbase, although I believe just scrapes XML content as there is no API. See development on GitHub for treebase here, and for rfishbase here. Carl has some tutorials on treebase and rfishbase at his website here, and we have an official rOpenSci tutorial for treebase here. Basically, these two R packages let you search and pull down data from Treebase and Fishbase - pretty awesome. This improves workflow, and puts your data search and acquisition component into your code, instead of being a bunch of mouse clicks in a browser. ...

Tom Miller (a prof here at Rice) and Brian Inouye have a paper out in Ecology (paper, appendices) that confronts two-sex models of dispersal with empirical data. They conducted the first confrontation of two-sex demographic models with empirical data on lab populations of bean beetles Callosobruchus. Their R code for the modeling work is available at Ecological Archives (link here). Here is a figure made from running the five blocks of code in ‘Miller_and_Inouye_figures.txt’ that reproduces Fig. 4 (A-E) in their Ecology paper (p = proportion female, Nt = density). Nice! ...

So, I’ve blogged about this topic before, way back on 5 Jan this year. Matt Helmus, a postdoc in the Wootton lab at the University of Chicago, published a paper with Anthony Ives in Ecological Monographs this year (abstract here). The paper addressed a new statistical approach to phylogenetic community structure. As I said in the original post, part of the power of the PGLMM (phylogenetic generalized linear mixed models) approach is that you don’t have to conduct quite so many separate statistical tests as with the previous null model/randomization approach. ...

Carl Boettiger gave a talk on the topic of open science to incoming UC Davis graduate students. Here is the audio click here Here are the slides clickhere

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.org/, or in the comments below, or on twitter (@rOpenSci), what use cases you would like to see with the rnpn package. ...

Interesting talks/posters: Richard Lankau presented research on trade-offs and competitive ability. He suggests that during range expansion selection for increased intraspecific competitive ability in older populations leads to loss of traits for interspecific competitive traits due to trade-offs between these traits. Ellner emphatically states that rapid evolution DOES matter for ecological responses, and longer-term evolutionary patterns as well. [His paper on the talk he was giving came out prior to his talk, which he pointed out, good form sir] ...

Interesting talks/posters: Ethan White’s poster describing EcologicalData.org was of course awesome given my interest in getting data into the hands of ecologists over at rOpenSci.org. Ethan also has software you can download on your machine to get the datasets you want easily - EcoData Retriever. [rOpenSci will try to take advantage of their work and allow you to call the retriever from R] Carl Boettiger’s talk was awesome. He explained how we need better tools to be able to predict collapses using early warning signals. He developed a way to estimate the statistical distribution of probabilities of system collapse. Jennifer Dunne: Explained how she put together an ancient network from Germany. Bravo. Carlos Melian explained his model of network buildup that starts from individuals, allows speciation, and other evolutionary processes. Rachel Winfree told us that in two sets of mutualistic plant-pollinator networks in New Jersey and California, that the least connected pollinator species were the most likely to be lost from the network with increasing agricultural intensity. Dan Cariveau suggests that pollination crop services can be stabilized even with increasing agriculture intensity if in fact pollinator species respond in different ways. That is, some pollinators may decrease in abundance with increasing ag intensity, while other species may increase - retaining overall pollination services to crops.

Monday was a good day at ESA in Austin. There were a few topics I promised to report on in my blogging/tweeting. …focused on open source data. Carly Strasser’s presentation on guidelines for data management was awesome (including other talks in the symposium on Creating Effective Data Management Plans for Ecological Research). Although this was a good session, I can’t help but wish that they had hammered home the need for open science more. Oh well. Also, they talked a lot about how, and not a lot of why we should properly curate data. Still, a good session. One issue Carly and I talked about was tracking code in versioning systems such as Github. There doesn’t seem to be a culture of versioning code for analyses/simulations in ecology. But when we get there…it will be easier to share/track/collaborate on code. ...

Our development team would like to announce the launch of rOpenSci. As the title states, this project aims to create R packages to make open science more available to researchers. http://ropensci.org/ What this means is that we seek to connect researchers using R with as much open data as possible, mainly through APIs. There are a number of R packages that already do this (e.g., infochimps, twitteR), but we are making more packages, e.g., for Mendeley, PLoS Journals, and taxonomic sources (ITIS, EOL, TNRS, Phylomatic, UBio). ...

I will be blogging about the upcoming Ecological Society of America meeting in Austin, TX. I will focus on discussing talks/posters that: Have taken a cool approach to using data, or Have focused on open science/data, or Done something cool with R software, or Are just exciting in general I will also tweet throughout the meeting from @recology_ (yes the underscore is part of the name, recology was already taken). ...