How to perform diallel analysis in R? Diallel Analysis using the Griffing and Hayman approach is so common in plant breeding and genetics. I'm wondering if someone can share R worked example on Diallel Analysis. Is there any good referenced book which covered worked examples? Thanks
References:
Griffing B (1956) Concept of general and specific combining ability in relation to diallel crossing systems.  Aust J Biol Sci 9:463-493 [pdf]
Hayman BI (1954) The analysis of variance of diallel tables.  Biometrics 10:235-244 [JSTOR]
Hayman BI (1954) The theory and analysis of diallel crosses.  Genetics 39:789-809 [pdf]
 A: There is beta package plantbreeding, which can do diallel analysis.  
https://r-forge.r-project.org/projects/plantbreeding/
They has a blog:
http://rplantbreeding.blogspot.com/ 
The following is example from this package:
require(plantbreeding)
 data(fulldial) 
 out <-diallele1(dataframe = fulldial, male = "MALE", female = "FEMALE",  
 progeny = "TRT", replication = "REP", yvar = "YIELD" )

print(out) 
out$anvout # analysis of variance 
    out$anova.mod1 # analysis of variance for GCA and SCA effects 
out$components.model1 # model1 GCA, SCA and reciprocal components 
    out$gca.effmat # GCA effects
out$sca.effmat # SCA effect matrix 
    out$reciprocal.effmat # reciprocal effect matrix 

out$varcompare  # SE for comparisions 
    out$anovadf.mod2   # ANOVA for model 2
out$varcomp.model2  # variance components for model 2 

A: I think it's unlikely that you'll find worked examples in R for the analysis of diallels.
I did find some references for diallel analysis in SAS (e.g., here, and there's a chapter on DIALLEL-SAS in the book Handbook of formulas and software for plant geneticists and breeders).
A: There's a nice worked example in the book Statistical and Biometrical Techniques in Plant Breeding by Jawahar R. Sharma on about page 184.  Visible in Google books. 
