Blog Archives

I Work For The Internet !

December 13, 2011
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I Work For The Internet !

UPDATE: code and figure updated at 1150 am CST.The site I WORK FOR THE INTERNET is collecting pictures and first names (last name initials only) to show collective support against SOPA (the Stop Online Piracy Act).  Please stop by their site and a...

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LondonR meetings presentations

December 11, 2011
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LondonR meetings presentations

Three presentations uploaded on LondonR meetings website.  I especially enjoyed the JD Long presentation on the seque package for simulations using Amazon's EC2.

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rOpenSci won 3rd place in the PLoS-Mendeley Binary Battle!

November 30, 2011
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rOpenSci won 3rd place in the PLoS-Mendeley Binary Battle!

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/ropensciWe entered two of our R packages for integrating with ...

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My talk on doing phylogenetics in R

November 18, 2011
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My talk on doing phylogenetics in R

I gave a talk today on doing very basic phylogenetics in R, including getting sequence data, aligning sequence data, plotting trees, doing trait evolution stuff, etc.Please comment if you have code for doing bayesian phylogenetic inference in R.  ...

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Use case: combining taxize and rgbif

November 1, 2011
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Use case: combining taxize and rgbif

Sure thing….this is just the sort of thing for which rOpenSci is being built. A colleague of mine recently saw our packages in development and thought, “Hey, that could totally make my life easier.”   What was made easier you ask?   This was his situation: He had a list of ca. 1200 species of

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My little presentation on getting web data through R

October 28, 2011
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My little presentation on getting web data through R

With examples from rOpenSci R packages. p.s. I am no expert at this...Web data from R View more presentations from schamber

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Two new rOpenSci R packages are on CRAN

October 27, 2011
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Two new rOpenSci R packages are on CRAN

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 cont...

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Two-sex demographic models in R

October 26, 2011
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Two-sex demographic models in R

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...

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New food web dataset

October 14, 2011
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New food web dataset

So, there is a new food web dataset out that was put in Ecological Archives here, and I thought I would play with it. The food web is from Otago Harbour, an intertidal mudflat ecosystem in New Zealand. The web contains 180 nodes, with 1,924 links. Fu...

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Phylogenetic community structure: PGLMMs

October 13, 2011
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Phylogenetic community structure: PGLMMs

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 addres...

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