Blog Archives

smoothScatter in base R

October 2, 2009
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smoothScatter in base R

smoothScatter function is now available also in base R - in the recommended package graphics that is shipped with R. Originally this function was in the genepplotter package from Bioconductor. I really like it since it can nicely plot large datasets. B...

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Fitting lactation curves/functions in R

September 3, 2009
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It is quite some time ago since I wrote a set of lactation curves/functions in R. I put those functions in the animSci package. However, the package is in a mess for quite some time now - I was adding some new functions, but did not have time to finish the job properly. This is also the reason...

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Additive vs. dominance two-allele genetic model by DIC

August 7, 2009
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Two-allele model has alleles A1 and A2 and genotypes A1A1, A1A2, and A2A2. This model can be fitted using only additive effect (restricted model) or additve+dominance effect. (full model) The later model has one parameter more than the former. I was using this model lately and got weird DIC results - the full model had less number...

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bugsparallel

June 18, 2009
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bugsparallel is a Metrum Institute project to run BUGS (via R2WinBUGS) in parallel - McMC is an application, where parallel runs can be used very efficientlly. Here is the code for one example using bugsparallel.Some usefull links:Rosenthal, Parallel c...

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Embeding fonts in figures produced by R

May 27, 2009
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Some publishers insist that we embed (include) the fonts in each figure. Here is a set of links regarding this issue for figures produced by R:http://tolstoy.newcastle.edu.au/R/help/05/01/10779.htmlhttps://stat.ethz.ch/pipermail/r-help/2006-October/114...

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Inference for R

April 8, 2009
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I got a message from Inference for R team. Their work is interesting, especially if you are bound to MS Excel and Word environment! It would be great if they would also support OpenOffice. They "benefit" from open source R and it would be great if they...

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R graphics: margins are way to large

February 22, 2009
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R graphics: margins are way to large

For me R has a very nice and powerfull capabilities for graphics (for example see this gallery). However, I dislike the default setting for margins and placement of axis numbers and labels. Since I always forget the setting of parameters I prefer I am adding this post. For example: library(package="MASS")Sigma mu tmp plot(tmp, xlab="X variable (unit)", ylab="Y variable...

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Illinois long-term selection experiment for oil and protein in corn

February 22, 2009
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Illinois long-term selection experiment for oil and protein in corn

Researchers at the University of Illinois are conducting one of the longest experiments in biology - Illinois long-term selection experiment for oil and protein in corn. The experiment started in 1896 and is still active! In esence they are selecting l...

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R in SAS

February 15, 2009
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R in SAS

Another "proof" that R definitely is one of mainstream statistical packages is the news that SAS will provide an interface to R via SAS/IML Studio (today known as SAS Stat Studio).

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Fitting Legendre (orthogonal) polynomials in R

February 10, 2009
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Fitting Legendre (orthogonal) polynomials in R

Frederick Novomestky packaged a series of orthogonal polynomials in the orthopolynom R package. However, his functions can not be used "directly" in a statistical model, say in lm(). There is no need to use functions from orthopolynom package, since th...

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