Blog Archives

Adjust branch lengths with node ages: comparison of two methods

April 10, 2011
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Adjust branch lengths with node ages: comparison of two methods

Here is an approach for comparing two methods of adjusting branch lengths on trees: bladj in the program Phylocom and a fxn written by Gene Hunt at the Smithsonian.Get the code and example files here: http://wp.me/PRT1F-2vGet phylocom here: http:/...

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Phylometa from R – UDPATE

April 1, 2011
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Phylometa from R – UDPATE

A while back I posted some messy code to run Phylometa from R, especially useful for processing the output data from Phylometa which is not easily done. The code is still quite messy, but it should work now. I have run the code with tens of different d...

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basic ggplot2 network graphs – ver2

March 23, 2011
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basic ggplot2 network graphs – ver2

I posted last week a simple function to plot networks using ggplot2 package. Here is version 2. I still need to work on figuring out efficient vertex placement.Changes in version 2:-You have one of three options: use an igraph object, a matrix, or a da...

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basic ggplot2 network graphs

March 17, 2011
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basic ggplot2 network graphs

I have been looking around on the web and have not found anything yet related to using ggplot2 for making graphs/networks. I put together a few functions to make very simple graphs. The bipartite function especially is not ideal, as of course we only w...

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Five ways to visualize your pairwise comparisons

March 5, 2011
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Five ways to visualize your pairwise comparisons

In data analysis it is often nice to look at all pairwise combinations of continuous variables in scatterplots. Up until recently, I have used the function splom in the package lattice, but ggplot2 has superior aesthetics, I think anyway.Here a fe...

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Phenotypic selection analysis in R

February 24, 2011
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Phenotypic selection analysis in R

I have up to recently always done my phenotypic selection analyses in SAS. I finally got some code I think works to do everything SAS would do. Feedback much appreciated!########################Selection analyses#############################install.pac...

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Troubling news for the teaching of evolution

February 9, 2011
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Troubling news for the teaching of evolution

A recent survey reported in Science ("Defeating Creationism in the Courtroom, but not in the Classroom"),  suggests that high school teachers are not teaching evolution to the fullest extent, say, that grammar is being taught in the English c...

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Good riddance to Excel pivot tables

January 30, 2011
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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)&nbsp...

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R and Google Visualization API: Fish harvests

January 17, 2011
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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=0Aq6aW8n11tS_dFRySXQzYkppLXFaU2F5aC04d19ZS0E&hl=en################# Fish harvest data...

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R and Google Visualization API: Wikispeedia

January 17, 2011
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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://grou...

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