Embeding fonts in figures produced by R

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.html
• https://stat.ethz.ch/pipermail/r-help/2006-October/114751.html
• https://stat.ethz.ch/pipermail/r-help/2005-April/069208.html
• http://tolstoy.newcastle.edu.au/R/e6/help/09/03/8065.html
• http://tolstoy.newcastle.edu.au/R/e5/help/08/09/1874.html

Generation interval calculation example

Here is a nice sheet with example of generation interval calculation in a flock of sheep.

Fitting pedigree based mixed models in BUGS software

Bellow is my abstract for talk at joint congress of SBD and SGD at Otočec. I will show how BUGS (Bayesian Using Gibbs Sampling) software can be used to fit the so called animal model. Now I need to prepair the talk and perhaps even write a short communication for some journal. Added 2009-09-20: The talk is available here.

Pedigree based mixed model (commonly called animal model) is an important class of statistical models for inference of quantitative genetic parameters in various fields such as animal and plant breeding, evolutionary biology and human genetics. In last years Bayesian statistics has been introduced to a set of standard statistical procedures of a quantitative geneticists' toolbox, due to the ever increasing complexity of fitted models. While several specific programs can be used to fit animal model using Bayesian approach, none of them provide and easy to use and flexible environment for the development and testing of models. It is common to use favourite programming language to develop the needed programs, but this requires a considerable amount of programming and statistical skills. A viable alternative is to use general purpose statistical packages. BUGS (Bayesian Using Gibbs Sampling) is a popular and fairly flexible program for the Bayesian analysis of complex statistical models using Markov Chain Monte Carlo methods. Recently two reports of fitting animal model in BUGS were given, but both failed to provide a generic procedure that can be used independently of the collected data. Here, a generic description of animal model is presented using the concept of graphical models. This description was translated to BUGS language and fitted to a small example. Comparison with other programs revealed the validity of a new procedure. Tests with other data sets showed that BUGS can be used to efficiently fit animal model for medium sized data sets. Using these results quantitative geneticists can now easily use Bayesian approach to fit animal model in BUGS.

Genetic architecture of quantitative traits in mice, flies, and humans

Flint and MacKay published a paper: "Genetic architecture of quantitative traits in mice, flies, and humans". I think it is now is clear that revolutionary ideas that were spured by the field of molecular genetics are still far from reality. There surely is a lot of progress, but also at considerable investments.

Those interested in quantitative genetics might also be interested in:

• Shortage of quantitative geneticists in animal breeding

• Data and Theory Point to Mainly Additive Genetic Variance for Complex Traits

SAS goes with sparse matrices

SAS has introduced experimental procedure HPMIXED (High Performance MIXED) in version 9.2. This is a welcome addition and now SAS could probably solve the problem I encountered lately with a large mixed model described here. I really like R and its community (which is getting bigger and bigger and more and more connected to other communities!), but I must say that for me SAS has made quite some important moves lately - see here, here, and here.

Statistics for Molecular Genetics

Nice notes about Statistics for Molecular Genetics by Karin Dorman.

Genes for cowboys

I rally like the title of this "material": Genes for cowboys. I still need to parse the content.

Video posnetki povezani s čebelami

Danes sem naletel na zgledno urejeno spletno stran ČEBELARSTVO Grega Lužar - tipa sploh ne poznam, tako da mu ne delam reklame. Na spletni strani je kar nekaj zanimivih video posnetkov opravil/dogodkov, ki jih sam še nikoli nisem videl:

• Razno
  
• Točenje medu
• Pridobivanje matičnega mlečka
  
• Vzreja čebeljih matic

Inference for R

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 would also provide a solution for open source "office".

Test for scrapie in goats

See here.