November 2008

First and easy steps with R and Sweave

November 28, 2008 | :)-k

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 ... [Read more...] plays with cacheSweave

November 26, 2008 | Gregor Gorjanc

I have added support for caching to 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 | Jeremy Leipzig

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 ... [Read more...]

Use anchoring to lose years off your age

November 21, 2008 | Diego

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 | :)-k

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... [Read more...]

Plot symbols in R

November 18, 2008 | Yu-Sung Su

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 ... [Read more...]

Call C from R and R from C

November 17, 2008 | Forester

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 ... [Read more...]

Sweave Engine for TeXShop

November 17, 2008 | cameron

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 ... [Read more...]

Using the booktabs package with Sweave and xtable

November 16, 2008 | cameron

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 ... [Read more...]

R function to reverse and complement a DNA sequence

November 13, 2008 | fabiomarroni

Warning!! This post is intended for documentation only. I would like to remind everyone (me in first place!) that the comp() function of the (seqinr) package can complement a DNA sequence, and rev() function of Rbase can reverse a character vector. Using a combination of the two you can reverse, ... [Read more...]

Saving a Workspace

November 11, 2008 | R Tips

R will can save the users workspace at the end of a session so that he can take it up again where he left off. I personally don't like doing this but there are times when one would want to save their work, especially after complex and time consuming co... [Read more...]

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