Posts Tagged ‘ Software ’

Value of an R object in an expression

December 15, 2010
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Value of an R object in an expression

Just wanted to create an expression, existing of some mathematical annotation and a value of an R object. Wasn't that intuitive!

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Homage to floating points

November 22, 2010
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I recently got very close to the floating point trap, again, so here is a little tribute with some small examples!

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Installing rgdal on Mac OS X

November 2, 2010
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Installing rgdal on Mac OS X

After running a spatial data analysis with R session today, it became apparent that there are one or two teething problems installing the important rgdal package on Mac OS X operating systems. The usual install.packages(“rgdal”) won’t work. My colleague Jon Reades did some digging around to find this solution. I have tested it and it

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highlight R syntax in wordpress using wp-codebox

October 10, 2010
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Tal Galili’s blog post mentioned that WP-Syntax can highlight R codes. I downloaded the modified version of WP-Syntax in his blog site. The plugin throw an error when activated. I did not try the original version hosted in WordPress. I found that WP-CodeBox use GeShi for syntax highlighting as WP-Syntax does.I used this plugin when I posted perl codes, but...

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highlight R syntax in wordpress using wp-codebox

October 10, 2010
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Tal Galili’s blog post mentioned that WP-Syntax can highlight R codes. I downloaded the modified version of WP-Syntax in his blog site. The plugin throw an error when activated. I did not try the original version hosted in Wordpress. I found that WP-CodeBox use GeShi for syntax highlighting as WP-Syntax does.I used this plugin when I posted perl codes,...

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All code on GGD is Free (Open Source BSD)

July 7, 2010
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At the request of a commenter I just wanted to clarify that any code released here for R or anything else is free and open source unless specifically stated otherwise. The open source BSD license for any code on GGD can be found on this copyright page.

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Must Have Software

May 28, 2010
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Having worked with Unix (BSD, HPUX, IRIX, Linux and OSX), Windows (NT4, 2000, XP, Vista and 7) for quite a while I have seen a lot of different software tools. I would like to quickly exhibit my “must have” list. These are the packages that I find to be the single “must have offerings” in Related posts:

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Mixed linear model approach adapted for genome-wide association studies

May 6, 2010
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A few weeks ago I covered an R package for efficient mixed model regression that is capable of simultaneously accounting for both population stratification and relatedness to compute unbiased estimates of standard errors and p-values for genetic associ...

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Efficient Mixed-Model Association in GWAS using R

April 13, 2010
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I recently did an analysis for the eMERGE network where I had lots of individuals from a small town in central Wisconsin where many of the subjects were related to one another. The subjects could not be treated as independent, but I could not use a fam...

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ProbABEL – R package for GWAS data imputation

April 6, 2010
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I've been using GenABEL for some time now for GWAS analysis using related individuals. It has an excellent set of functions for estimating a kinship matrix from a dense marker panel and then using this in a linear mixed effects model to allow for relat...

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