Monthly Archives: November 2008

First and easy steps with R and Sweave

November 28, 2008
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First and easy steps with R and Sweave

What really sold me to the idea of using Sweave and therefore (re)learning LaTeX was the idea of Reproducible Research. Charlie Geyer has put together some examples how to mix and match R and LaTeX with Sweave. Today's goal therefore is to run his examples and to see, what problems I run into :)Allright, if you all...

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Sweave.sh plays with cacheSweave

November 26, 2008
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Sweave.sh plays with cacheSweave

I have added support for caching to Sweave.sh script as implemented in cacheSweave R package written by Roger D. Peng. Now, one can set caching on for chunks that are time consuming (data import, some calculations, ...) and the Sweaving process will r...

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Calculating an N50 from Velvet output

November 25, 2008
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In sequencing circles the N50 length is a useful heuristic for judging the quality of an assembly. Here is my definition of N50 length, which you may or may not find intuitive: N50 length is the length of the shortest contig such that the sum of contigs of equal length or longer is at least 50% of the total length...

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Use anchoring to lose years off your age

November 21, 2008
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Use anchoring to lose years off your age

It is well known in psychology that the way a question is asked can strongly influence the answer. For example, if you spin a random number wheel and later have people guess the proportion of United Nations countries that are African, their answers clo...

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Setting up Textmate to use R

November 21, 2008
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Setting up Textmate to use R

After becoming frustrated using the StatET plugin for Eclipse on my Mac (sometimes the R console would start and sometimes not), I decided to use Textmate instead. Textmate allows you to install extra bundles which are plug-ins to add some new function...

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Plot symbols in R

November 18, 2008
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In the plot environment, the "pch" parameter decides the symbol of your output. There are about 130 symbols hard coded and passed into "pch."However, there are still some symbols that are not in these 130 pch's. For instance, there is no checkmark. To plot checkmark or other symbols, we can use symbol() in the expression()...

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Call C from R and R from C

November 17, 2008
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Several years ago, while a research associate at the University of Chicago, I had the privilege of sitting in on a course taught by Peter Rossi: Bayesian Applications in Marketing and MicroEconometrics. This course -- one I recommend to anyone at U Chicago who is interested in statistics -- was an incredibly clear treatment of Bayesian...

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Multivariate dependence with copulas

November 17, 2008
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Classes (S4) of commonly used copulas including elliptical (normal and t), Archimedean (Clayton, Gumbel, Frank, and Ali-Mikhail-Haq), extreme value (Husler-Reiss and Galambos), and other families (Plackett and Farlie-Gumbel-Morgenstern). Methods for d...

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Sweave Engine for TeXShop

November 17, 2008
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Sweave Engine for TeXShop

Sweave is an awesome utility for including the output of R code in a LaTeX document which I have started using regularly. TeXShop is my favorite editor/viewer for LaTeX under Mac OS X for many reasons. One of which is the speed of the edit -> compile -> view process which it enables. Therefore, I

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Using the booktabs package with Sweave and xtable

November 16, 2008
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Using the booktabs package with Sweave and xtable

The xtable package in R can output R data as latex tables. Used in conjunction with Sweave it is possible to automatically generate tables in a report. Needless to say this provides a really appealing possibility of never typing data into a table again. The only problem is that I think the default latex tables

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