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 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....

October 26, 2011 · 1 min · Scott Chamberlain

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 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....

October 13, 2011 · 1 min · Scott Chamberlain

PLoS journals API from R: "rplos"

The Public Libraries of Science (PLOS) has an API so that developers can create cool tools to access their data (including full text papers!!). Carl Boettiger at UC Davis and I are working on R functions that use the PLoS API. See our code on Github here. See the wiki at the Github page for examples of use. We hope to deploy rplos as a package someday soon. Please feel free to suggest changes/additions rplos in the comments below or on the Github/rplos site....

June 21, 2011 · 1 min · Scott Chamberlain

How to fit power laws

A new paper out in Ecology by Xiao and colleagues (in press, here) compares the use of log-transformation to non-linear regression for analyzing power-laws. They suggest that the error distribution should determine which method performs better. When your errors are additive, homoscedastic, and normally distributed, they propose using non-linear regression. When errors are multiplicative, heteroscedastic, and lognormally distributed, they suggest using linear regression on log-transformed data. The assumptions about these two methods are different, so cannot be correct for a single dataset....

June 7, 2011 · 1 min · Scott Chamberlain

Species abundance distributions and basketball

A post over at the Phased blog ( highlights a recent paper in PLoS One by Robert Warren et al. Similar results were obtained in a 2007 Ecology Letters paper by Nekola and Brown, who showed that abundance distributions found in ecology are similar to those found for scientific citations, Eastern North American precipitation, among other things. A similar argument was made by Nee et al. in 1991 (in the journal PRSL-B)....

March 13, 2011 · 2 min · Scott Chamberlain

Phylogenetic analysis with the phangorn package: an example

The phangorn package is a relatively new package in R for the analysis and comparison of phylogenies. See here for the Bioinformatics paper and here for the package. Here is an example of using phangorn from getting sequences to making phylogenies and visualizing them:Getting sequences from GenbankMultiple alignmentMaximum likelihood tree reconstructionVisualizing treesVisualizing trees and traitsMake fake traits:Visualize them on trees:

February 21, 2011 · 1 min · Scott Chamberlain

New approach to analysis of phylogenetic community structure

Anthony Ives, of University of Wisconsin-Madison, and Matthew Helmus of the Xishuangbanna Tropical Botanical Garden, present a new statistical method for analyzing phylogenetic community structure in an early view paper in Ecological Monographs. See the abstract here. Up to now, most phylogenetic community structure papers have calculated metrics and used randomization tests to determine if observed metrics are different from random. The approach of Ives and Helmus fits models to observed data, instead of calculating single metrics....

January 5, 2011 · 1 min · Scott Chamberlain