Thursday, August 11, 2011

Wednesday at #ESA11

Recology has moved, go to http://recology.info/2011/08/wednesday-at-esa11

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, August 8, 2011

    Monday at #ESA11

    Recology has moved, go to http://recology.info/2011/08/monday-at-esa11

    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.

    ...used R software. David Jennings talked about a meta-analysis asking if phylogenetic distance influences competition strength in pairwise experiments. David used the metafor package in R to do his meta-analysis. Good form sir.

    ...did cool science. Matt Helmus presented a great talk on phylogenetic species area curves (likely using R, or Matlab maybe?).


    p.s. We launched rOpenSci today.


    Oddities:
    • The Tilman effect - Tilman's talk was so packed it looked like there was a line waiting to get into a trendy bar. Here's a picture (credit: Jaime Ashander). Bigger room next time anyone? 
    • Wiley came out with an open source journal called Ecology and Evolution. This brings them to 3 open source journals (the other two are in other fields). We (rOpenSci) will attempt to hand-shake with these journals. 
    • The vegetarian lunch option was surprisingly good. Nice. 

    (#ESA11) rOpenSci: a collaborative effort to develop R-based tools for facilitating Open Science

    Recology has moved, go to http://recology.info/2011/08/esa11-ropensci-collaborative-effort-to_08

    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).

    Importantly, we are creating a package called rOpenSci, which aims to integrate functions from packages for individual open data sources.

    If you are somewhat interested, follow our progress on our website, on Twitter, or contact us. If you are really^2 interested you could go to Github and contribute. If  you are really^3 interested, join our development team.