Monthly Archives: November 2009

Quantitative link strength for APE cophyloplot

November 17, 2009
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Quantitative link strength for APE cophyloplot

Just add a third column with link strength to the association matrix plotCophylo2 <- function (x, y, assoc = assoc, use.edge.length = use.edge.length, space = space, length.line = length.line, gap = gap, type = type, return = return, col = col, show.tip.label = show.tip.label, font = font) { if(ncol(assoc)==2) { assoc <- cbind(assoc,rep(1,nrow(assoc))) } res

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swfDevice is nearing completion

November 17, 2009
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My new R package, swfDevice, is getting close to its first release. This package enables native R graphics output as swf (flash) files. It also as the ability to create animations with player controls. The main project page is here and the results of the test suite are here. Here are some samples: http://swfdevice.r-forge.r-project.org/swfDevice_test29.swf http://swfdevice.r-forge.r-project.org/swfDevice_test28.swf

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R tip: Extracting median from survfit object

November 17, 2009
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A colleague wanted to extract the median value from a survival analysis object, which turned out to be a pain as the value is not stored in the object, but calculated on the fly by a print method.> library(survival)> fit > survfit(fit)Call: survfit(formula = fit)records n.max n.start events median 0.95LCL 0.95UCL ...

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R tip: Extracting median from survfit object

November 17, 2009
By

A colleague wanted to extract the median value from a survival analysis object, which turned out to be a pain as the value is not stored in the object, but calculated on the fly by a print method. > library(survival)> fit > survfit(fit)Call: survfit(formula = fit)records n.max n.start events median 0.95LCL 0.95UCL ...

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R functions for Dienes (2008) Understanding Psychology as a Science

November 17, 2009
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I recently wrote a review of Understanding psychology as a science: an introduction to scientific and statistical inference by Zoltan Dienes (2008). Dienes' book covers Neyman-Pearson null hypothesis significance testing, Bayesian inference and the lik...

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Seminar: Reproducible Research with R, LaTeX, & Sweave

November 16, 2009
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Theresa Scott, instructor of the previously mentioned R workshop and weekly R clinic, is giving a lecture entitled "Reproducible Research with R, LaTeX, & Sweave" in MRB III, room 1220, this Wednesday 11/18 at 1:30.  You can see more details about the lecture here. Looks like her slides as well as much more introductory material on R, Latex, and Sweave...

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Infomaps using R – Visualizing German unemployment rates by district on a map

November 16, 2009
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Infomaps using R – Visualizing German unemployment rates by district on a map

Lately, David Smith from REvolution Computing set out to challenge the R community with the reprocuction of a beautiful choropleth map (= multiple regions map/thematic map) on US unemployment rates he had seen on the Flowing Data blog. Here you can find the impressing results. Being a fan of beautiful visualizations I tried to produce

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R in Action – early thoughts

November 16, 2009
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R in Action – early thoughts

I was invited to review the book R in Action written by Rob Kabacoff. Since I consider the Quick-R website, created by the same smart guy, one of the most valuable resources about R, It is both an honor and a pleasure to have the opportunity to take an...

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R in Action – early thoughts

November 16, 2009
By
R in Action – early thoughts

I was invited to review the book R in Action written by Rob Kabacoff. Since I consider the Quick-R website, created by the same smart guy, one of the most valuable resources about R, It is both an honor and a pleasure to have the opportunity to take an...

Read more »

The Top Scores for Canabalt, Take 2

November 15, 2009
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The Top Scores for Canabalt, Take 2

Introduction As promised on Thursday, here’s my second pass at a statistical analysis of Canabalt scores. There are some useful results I’ll present right at the start, and then there are some results that are more or less worthless, except that working through my own mistakes helped me to think more clearly about statistical modeling in

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