Publications by Scott Chamberlain
A new blog about using R for ecology and evolution
I am starting this blog not because I am a seasoned code writer, but because I am learning how to use R specifically for ecology and evolution, and figured many others might have the same questions I have. If I find cool solutions I will post them here for all to view, criticize, improve, etc. Related To leave a comment for the auth...
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Phylogenetic meta-analysis in R using Phylometa
Here is some code to run Phylometa from R. Phylometa is a program that conducts phylogenetic meta-analyses. The great advantage of the approach below is that you can easily run Phylometa from R, and manipulate the output from Phylometa in R. Phylometa was created by Marc Lajeunesse at University of South Florida, and is described in h...
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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 calcul...
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Ecological networks from abundance distributions
Another grad student and I tried recently to make a contribution to our understanding of the relationship between ecological network structure (e.g., nestedness) and community structure (e.g., evenness)……Alas, I had no luck making new insights. However, I am providing the code used for this failed attempt in hopes that someone may...
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R and Google Visualization API
R interfaces with the powerful Google Visualization API with the package googleVis (see here). It’s relatively easy to convert your graphics in R to interactive graphics to post on a web browser. And the graphics are quite nice, as seen below in a simple graph of some of my data collected from this summer on seed predation to Helian...
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just for fun: Recovery.gov data snooping
Okay, so this isn’t ecology related at all, but I like exploring data sets. So here goes…Propublica has some awesome data sets available at their website: http://www.propublica.org/tools/I played around with their data set on Recovery.gov (see hyperlink below in code). Here’s some figures:Mean award amount, ranked by mean amount, and also c...
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Bipartite networks and R
Earlier, I posted about generating networks from abundance distributions that you specify. If this post was interesting, check out Jeff Kilpatrick’s website, where he provides code he produced in R and Octave to compare real bipartite networks to ones generated based on ecological variables measured in the field (in our case it was ...
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R and Google Visualization API: Wikispeedia
Wikispeedia is a website trying to gather all speed limit signs on Earth. I recently created a Google Visualization for some of their data, specifically on speed limit signs that change speed throughout the day.Check it out here: http://groups.google.com/group/wikispeedia/browse_thread/thread/c9c712125a597b16Here is how to see and ...
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R and Google Visualization API: Fish harvests
I recently gathered fish harvest data from the U.S. National Oceanic and Atmospheric Administarion (NOAA), which I downloaded from Infochimps. The data is fish harvest by weight and value, by species for 21 years, from 1985 to 2005. Here is a link to a google document of the data I used below: https://spreadsheets.google.com/ccc?key=...
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Good riddance to Excel pivot tables
Excel pivot tables have been how I have reorganized data…up until now. These are just a couple of examples why R is superior to Excel for reorganizing data:################ Good riddance to pivot tables ############ library(reshape2) library(plyr) dataset <- data.frame(var1 = rep(c("a","b","c","d","e","f"), each = 4), var2 = rep(...
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