Three presentations uploaded on LondonR meetings website. I especially enjoyed the JD Long presentation on the seque package for simulations using Amazon's … Continue reading →
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 PLoS Journals (rplos) and Mendeley (RMendeley) … Continue reading →
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. I know phyloch has function mrbayes, but can't … Continue reading →
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. … Continue reading →
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 … Continue reading →
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 … Continue reading →
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. Fun stuff...igraph, default layout plotigraph, … Continue reading →
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 … Continue reading →
Regular expressions are a powerful in any language to manipulate, search, etc. data. For example:> fruit <- c("apple", "banana", "pear", "pineapple")> fruit[1] "apple" "banana" "pear" "pineapple"> grep("a", fruit) # there is an "a" in each of the words[1] 1 2 3 4> > … Continue reading →
Rolf Lohaus, a Huxley postdoctoral fellow here in the EEB dept at Rice University, gave our R course a talk on basic visualizations in R this … Continue reading →
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 … Continue reading →
There is an awesome position opening up for an assistant professor in systematics at the University of Vermont. Below is the announcement, and see the original post at the Distributed Ecology blog. Why is this related to R? One can do a lot of systematics work in R, including retrieving scientific … Continue reading →
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 … Continue reading →
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