Blog Archives

gRain: genetics example

April 14, 2011
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gRain: genetics example

gRain is an R package for "probability propagation in graphical independence networks, also known as probabilistic expert systems (which includes Bayesian networks as a special case)". This package caught my attention because some genetic models can b...

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Nice simple notes on running R in parallel by Geyer

March 15, 2011
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Here, by Charles J. Geyer.

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Nice simple notes on running R in parallel by Geyer

March 15, 2011
By

Here, by Charles J. Geyer.

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Converting strsplit() output to a data.frame

January 28, 2011
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R has a nice set of utilities to work with strings. Function paste is surely one among these. It can be used to "glue" several strings with optional separator. The following example shows how paste can be used to create a new variable in a dataset:dat (dat$z Today I was in a situation where I only had column...

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Converting strsplit() output to a data.frame

January 28, 2011
By

R has a nice set of utilities to work with strings. Function paste is surely one among these. It can be used to "glue" several strings with optional separator. The following example shows how paste can be used to create a new variable in a dataset: dat (dat$z Today I was in a situation where I only had column...

Read more »

ASReml-R: Storing A inverse as a sparse matrix

December 18, 2010
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I was testing ASReml-R program (an R package that links propriety ASReml binaries that can be used only with valid licence) this week and had to do some manipulations with the numerator relationship matrix (A). ASReml-R provides a function (asreml.Ainverse) that can create inverse of A directly from the pedigree as this inverse is needed in pedigree based...

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ASReml-R: Storing A inverse as a sparse matrix

December 18, 2010
By

I was testing ASReml-R program (an R package that links propriety ASReml binaries that can be used only with valid licence) this week and had to do some manipulations with the numerator relationship matrix (A). ASReml-R provides a function (asreml.Ainverse) that can create inverse of A directly from the pedigree as this inverse is needed in pedigree based...

Read more »

IPSUR book used LyX-Sweave

July 28, 2010
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Jay Kerns wrote a book titled "Introduction to Probability and Statistics Using R" or IPSUR for short. He has put up a web site for the book and Rcmdr plugin. There are at least two very important points from my side (I did not read the book, yet): 1. ...

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IPSUR book used LyX-Sweave

July 28, 2010
By

Jay Kerns wrote a book titled "Introduction to Probability and Statistics Using R" or IPSUR for short. He has put up a web site for the book and Rcmdr plugin. There are at least two very important points from my side (I did not read the book, yet): 1. ...

Read more »

Drawing pedigree examples using the kinship R package

June 30, 2010
By
Drawing pedigree examples using the kinship R package

I have previously provided sort of an overview about plotting the pedigrees, then specifically using the Graphiviz, while I have lately used the TikZ LaTeX (see slides 11-15) system (see more example). The later gives great (beautiful) results, but at the cost of writing TikZ code - it is not that horible, just time consuming...

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