While reading UseR conference abstracts I came across this sentence: "Sugarcane is polypoid, i.e., has 8 to 14 copies of every chromosome, with individual alleles in varying numbers." Vau! This generates really complex genotype system. Say we have bial...
Additive genetic covariance between individuals is one of the key concepts in (quantitative) genetics. When doing the prediction of additive genetic values for pedigree members, we need the inverse of the so called numerator relationship matr...
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...
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 ...
Andrej Blejec has a very nice R demo of Galton's quincunx (link1, link2). It is a bit tedious to copy the code from PDF to R console, but it is worth the effort as the demo simulation clearly shows the nature of quincunx. After a bit of search I also f...
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 us...
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...
Jarrod Hadfield published MCMCglmm package on CRAN. The package can fit generalised linear mixed models via MCMC methods. Bellow is the abstract from the vignette. The list of supported models is quite impressive. Nice job Jarrod! This is not the first...
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).