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The ggplot2 package can be used as an alternative to lattice for producing high quality graphics in R. The package provides a framework and hopefully simple interface to producing graphs and is inspired by the grammar of graphics. The main function for producing graphs in this package is qplot, which ... [Read more...]

Every year, I single out what I think are the Top Five open source projects. This year, there's only one hold-over from previous years, and it's likely that I'm just going to give it a Lifetime Achievement Award and pick five others next year. 5. NetBe... [Read more...]

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Named rjson, appropriately. It’s quite basic just now, but contains methods for interconversion between R objects and JSON. Something like this: __ library(rjson) __ data json json [1] "{\"a\":1,\"b\":2,\"c\":3}" __ cat(json, file="data.json") Use cases? I wonder if RApache could be used to build an API that serves ... [Read more...]

Well testing a bunch of samples for the largest population mean isn’t that common yet a simple test is at hand. Under the obvious title “The rank sum maximum test for the largest K population means” the test relies on the calculation of the sum of ranks under the ... [Read more...]

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Samtools and its BioPerl wrapper Bio::DB:Sam prefer to give read coverage on a depth per base pair basis. This is typically an array of depths, one for every position that has at least one read aligned. OK, works for me. But how can we quickly see which targets (... [Read more...]

While flirting around with previously mentioned ggplot2 I came across an incredibly useful set of functions in the plyr package, made by Hadley Wickham, the same guy behind ggplot2.  If you've ever used MySQL before, think of "GROUP BY", but here you can arbitrarily apply any R function to splits ... [Read more...]

LondonR Date: Tuesday 3rd November Time: 6pm – 9.30pm Venue: Shooting Star Public house, 129 City Rd London, EC1, United Kingdom +44 20 7929 6818 Introduction: Richard Pugh - mangosolutions 6.15pm: Richard Saldanha - R in the ... [Read more...]

WelshPerm [Read more...]

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Regular readers of this blog (yes, both of you!) may remember the computer/broadband/ directory that this post appears in as the collection of my Comcastic (yeah right) experiences with my ISP. But I think this week may top everything. I'll just... [Read more...]

mat.sort [Read more...]

Last week, I attended the 2006 UseR! conference: here is a (long) summary of some of the talks that took place in Vienna -- since there were up to six simultaneous talks, I could not attend all of them... In this note: 0. General remarks 1. Tutorial:... [Read more...]

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I have just uploaded the new version of my "Statistics with R": http://zoonek2.free.fr/UNIX/48_R/all.htmlThe previous version was one year and a half old, so in spite of the fact I have not had much time to devote to it in the past two years, ... [Read more...]

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R only does natural (neperian) log scales by default, and this is lame. Here is a simple code to do decimal log scale, pretty much a requirement for scientists… The force(x/y)lim options works for natural and log scales (for the later case, you need to specify the ... [Read more...]