# Monthly Archives: September 2013

## Regression on variables, or on categories?

September 30, 2013
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I admit it, the title sounds weird. The problem I want to address this evening is related to the use of the stepwise procedure on a regression model, and to discuss the use of categorical variables (and possible misinterpreations). Consider the following dataset > db = read.table("http://freakonometrics.free.fr/db2.txt",header=TRUE,sep=";") First, let us change the reference in our categorical variable  (just to...

## Which is the best "Flyover" state?

September 30, 2013
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If you were to hop into your personal aircraft, and plotted a straight line course taking off in one state and landing in the SAME state, how many other states might you fly over? On other words, what's the best state for "flyovers" of other states? Todd Schnieder from the Rapgenius engineering team answered that question using the R...

## How heavy is the Siberut macaque? A Bayesian phylogenetic approach

September 30, 2013
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Among-species comparisons can include phylogenetic information to account for non-independence arising from shared evolutionary history. Often, phylogenetic topologies and branch lengths are not known exactly, but are estimated with uncertainty. This uncertainty can be accounted for using methods recently described in a neat paper called Bayesian models for comparative analysis integrating phylogenetic uncertainty by Villemereuil et...

September 30, 2013
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This post is a follow up from my latest Things I Forget post on reading in shapefiles.  That post assumed that you already had access to all the relevant files (e.g. .shp, .shx, .prj, .dbf, etc.).  A task that I routinely need to do is locate shapefiles on a website, grab those files, and read

## A Bayesian Twist on Tukey’s Flogs

September 30, 2013
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In the last post I described flogs, a useful transform on proportions data introduced by John Tukey in his Exploratory Data Analysis. Flogging a proportion (such as, two out of three computers were Macs) consisted of two steps: first we “started” the proportion by adding 1/6 to each of the counts and then we “folded” it...

## ROC curves and classification

September 30, 2013
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To get back to a question asked after the last course (still on non-life insurance), I will spend some time to discuss ROC curve construction, and interpretation. Consider the dataset we’ve been using last week, > db = read.table("http://freakonometrics.free.fr/db.txt",header=TRUE,sep=";") > attach(db) The first step is to get a model. For instance, a logistic regression, where some factors were merged...

## eoda’s R-academy celebrates its third anniversary and is extending the extensive training program for R

September 30, 2013
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The free statistical programming language R becomes more and more popular, even in German speaking areas. This happens for various reasons. Besides from its performance, its quality and its open source character, R scores with its various possibilities for integration. Beyond that R offers a multitude of possibilities in the field of multivariate analysis methods.

September 30, 2013
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Along with the Rcpp 0.10.5 release yesterday, a new minor release 0.3.920.1 of RcppArmadillo came out. It is based on Conrad's Armadillo 3.920.0 plus a minor fix, and uses some of the new Rcpp features. Both package is now on CRAN and also in Debian....

## New version of lme4

September 30, 2013
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If you haven't realized it yet, a new version of lme4 (version 1.0-4) was released recently (Sept. 21). For an end-user like me, there were not many changes, but there were a few:No more using the @ operator. After a very helpful email exchange with Be...

## Testing R Packages

September 29, 2013
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This guy th3james claimed Testing Code Is Simple, and I agree. In the R world, this is not anything new. As far as I can see, there are three schools of R users with different testing techniques: tests are put under package/tests/, and a foo-test.Rout.save from R CMD BATCH foo-test.R; testing is done by comparing foo-test.Rout from R CMD check with your foo-test.Rout.save; R...