Openaccess

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. You could surely mash up data from both PLoS and Mendeley. That’s what’s cool about rOpenSci - we provide the tools, and leave it up to users vast creativity to do awesome things. 3rd place gives us a $1,000 prize, plus a Parrot AR Drone helicopter. ...

Ten Simple Rules for Open Access Publishers View more presentations from Philip Bourne

The O’Reilly Media Strata Summit has many interviews on YouTube (just search YouTube for it)Drew Conway is the author of a R packages, including infochimps, an R wrapper to the Infochimps API service. The YouTube video:

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

UPDATE: I put in an R tutorial as a Github gist below. Here is a short intro R talk I gave today…for what it’s worth… R Introduction View more presentations from schamber Here’s the tutorial in a GitHub gist: https://gist.github.com/1208321

FigShare - I very much like this idea of a place to put your data online that is NOT published. Dryad is a nice place for datastes linked with published papers, but there isn’t really a place for datasets that perhaps did not make the cut for a published paper, and if known to the scientific community, could potentially help resolve the “file-drawer” effect in meta-analyses. (wow, run on sentence) ...

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). ...