Monthly Archives: January 2010

Transitions and transversions in R

January 5, 2010
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Transitions and transversions in R

A couple of months ago I wrote the following R function to calculate the number of transitions and transversions between DNA sequences in an alignment. The function is fairly slow (an alignment of ~100 sequences, 800 bp in length takes around 30 second...

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Setting the HTML title tag in SAS ODS (the right way)

January 5, 2010
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Setting the HTML title tag in SAS ODS (the right way)

In our department and various places on the Intertubes, SAS programmers set the HTML title tag (which sets the title in web browsers and on search engines) in ODS using the headtext option: ods html headtext="<title>My great report</title>" /* wrong! */ file="foo.html"; This may work in some situations, but it’s ugly and wrong. To see

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Announcing r-ORM: A Pure R Object-Relational Mapper

January 5, 2010
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My apologies for the long break between posts. Before the end of this week I’ll return to my series of posts on image processing in R. In the intervening time, I’ve finished a piece of code that I’d like to officially release to the public. The code in question is a very minimal object-relational mapper

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Analyzing a FriendFeed group with Ruby and R

January 5, 2010
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Analyzing a FriendFeed group with Ruby and R

FriendFeed is a social media service, where groups of people can post interesting information from the Web, and "like" or comment posts from others. Statistical Bioinformatician Neil Saunders is a member of the "Life Scientists" group, and has posted an analysis of the group's activity in 2009 to his blog. He used Ruby and the FriendFeed API to extract...

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R Journal 1/2

January 5, 2010
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R Journal 1/2

R Journal 1/2 is out! Grab it from here.

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R Journal 1/2

January 5, 2010
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R Journal 1/2

R Journal 1/2 is out! Grab it from here.

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R: Memory usage statistics by variable

January 4, 2010
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R: Memory usage statistics by variable

Do you need a way to find out which individual variables in R consume the most memory? # create dummy variables for demonstration x <- 1:1000 y <- 1:10000 z <- 1:100000 # print aggregate memory usage statistics print(paste('R is using', mem...

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Example 7.20: Simulate categorical data

January 4, 2010
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Example 7.20: Simulate categorical data

Both SAS and R provide means of simulating categorical data (see section 1.10.4). Alternatively, it is trivial to write code to do this directly. In this entry, we show how to do it once. In a future entry, we'll demonstrate writing a SAS Macro (section A.8.1) and a function in R (section B.5.2) to do it...

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O’Reilly’s R is a Harpy Eagle

January 4, 2010
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O’Reilly’s R is a Harpy Eagle

Today marks the hardcopy availability of the first book dedicated to R from O'Reilly, R in a Nutshell. In the familiar O'Reilly style, the cover is adorned with an illustration of an animal, in this case a harpy eagle: The book is written by Joe Adler, a data analyst and the author of Baseball Hacks. In contrast to the...

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Welcome!

January 4, 2010
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Welcome to my new blog, Byte Mining! Data is all around us, all the time. It flows in from places you would least expect it, and more times that not, it remains in its original form untouched by human and machine. When data simply flows in and out of our lives, we miss out on the story that it...

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