A History of Markov Chain Monte Carlo

Robert and Casella wrote a paper with a title "A History of Markov Chain Monte Carlo--Subjective Recollections from Incomplete Data--". It is a nice reading. Beeing an animal breeder I of course liked the following footnote ;)

On a humorous note, the original Technical Report of this paper was called Gibbs for Kids, which was changed because a referee did not appreciate the humor. However, our colleague Dan Gianola, an Animal Breeder at Wisconsin, liked the title. In using Gibbs sampling in his work, he gave a presentation in 1993 at the 44th Annual Meeting of the European Association for Animal Production, Arhus, Denmark. The title: Gibbs for Pigs.


LaTeX Style and BiBTeX Bibliography Formats for Biologists: TeX and LaTeX Resources

AIPL writings and presentations

I noticed that researchers at AIPL (USA) are very active with the current hot topic in animal breeding - genomic (genomewide) selection (Meuwissen et al., 2001). I asked Paul VanRaden for a reprint and he has kindly pointed me to the website of AIPL with conference proceedings and presentations. These two sites are very valubale resource for study - not only forthe topic of genomic selection, but also for dairy cattle breeding!


Password remind flaw in Joomla! 1.5.x

One of my sites uses Joomla! and the last day the password of the admin was changed. Shit! I thought that I had an intruder. Carefull inspection showed that there was nobody on the server beside me - the hacker could have gained my user account, but I remember what I did the last time so only the password was changed. Now I found out that the hacker used password remind flaw. After upgrade, I logged into the DB and updates the password with MD5 hash obtained from Paj's Home: Crypto... site.

UPDATE jos_users SET password='MD5HASH' WHERE id='???';

Alternatively, I could use this

UPDATE jos_users SET password=PASSWORD('???') WHERE id='???';

but then it is better to remove the .mysql history file!



I was searching for some papers via Google and found a PDF file with a list of very fine reference on the topic of inbreeding. I discovered that the PDF file is hosted at Consang.net. I like te site! Read the summary if you are interested in the topic. They show a nice map showing level of inbreeding in humans as reported in the literature. I am linking the picture here to make the post more interesting ;)

Beside nice map, the site has also a Google map that shows the data (by country) that were used in the creation of the above map. I only checked some data and found out that (out of those I looked at) many refernces are quite old. Therefore, I am bit skeptical about the "validity" of the map for the present time. For example, Hans Rosling showed that there have been large changes in the world in last century. Well, the "mating system" in humans probably did not change that much, but I still have some doubts that the level of inbreeding in humans is so much higher in the Near East. This could be as well just my lack of knowledge. I would be happy if anyone can teach me;) Besides this data the site hosts a fine list or references.

Google pages / sites

I use Google page creator for hosting my website. However, this "application" will be replaced by Google Sites. They have posted a very nice tutorial, which shows the capabilities. I like it. Simple and easy to set a website.


Calculation of PrP genotype and NSP type probabilities in Slovenian sheep

Paper "Calculation of PrP genotype and NSP type probabilities in Slovenian sheep" is finnaly finnished. I will send it to the journal today. This is a sort of a companion paper to the previous one where the methods were derived and tested, while in this paper we used those methods on all sheep breed in the Slovenian breeding programme for sheep. Here is the abstract:

PrP genotype probabilities in ungenotyped Slovenian sheep were calculated. Altogether 36,083 ewes and rams of various breeds were included into the analysis. PrP genotype was known for 10,504 animals. Five different PrP alleles were present in the data. Pedigree and genotype data structure differed between breeds. Iterative allelic peeling with incomplete penetrance model was used for the calculation of genotype probabilities for each animal given the genotype data of relatives. Analyses were performed for each breed separately. Additionally, NSP (National Scrapie Plan) type probabilities and the average NSP type were calculated from the genotype probabilities. Results were presented for live animals only. There were no animals with additionally identified PrP genotype or NSP type with certainty. With 95 % probability PrP genotype was additionally identified for 0.0 to 5.7 % animals of different breeds. NSP type was additionally identified with the same probability for 0.0 to 34.9 % animals of different breeds. We maintain that the low number of additional identifications was due to: a large number of alleles, intermediate allele frequencies, data structure, a uniform prior, and the use of incomplete penetrance model. Additional identifications provided some cost savings, but did not prove useful in the selection for scrapie resistance of the entire populations. The average NSP type should be used instead, since it can be calculated for all animals and encompasses all information from genotype probabilities.


Some news about gdata R package

Here are some news for gdata R package:
  • new function cbindX to column bind object with different number of rows
  • write.fwf gains new argument width, additionally several enhancements were done internally to make sure that effect of unknown values (via argument na) on column widths are properly handled
  • changes are only available via SVN and in packaged form (source package, Windows MS package) - packages will be removed after the new version of gdata will be published at CRAN

Literature on connectedness

Denis Laloe has posted a list of papers about the connectedness. See also the results for Connectedness in International Genetic Evaluation (Interbull).