On Tuesday, December 16, 2014 1:32:19 PM UTC-6, Taylor Maxwell wrote: > > Pedigrees sounds like a good name. Will this package be able to generate > and manipulate standard kinship matrices? This is not my specialty but > familial data is pretty common and many standard association methods for > "unrelated" individuals have analogous method that need to take into about > the relationships among individuals that come with familial data. In > particularly the the kinship matrix is often a large sparse matrix that is > used as random effects in mixed linear models. The kinship package in R is > very useful for the construction and use of these matrices. With some > colleagues (who know the statistical theory better than I) we have > developed a methodology to look at simultaneous mean and variance effects > in unrelated individuals. We recently adapted it to use family data. We > were able to use the kinship package in R to construct the kinship matrix > (a sparse matrix) and applied our methodology with the help of their > "gchol" function to implement a generalized Cholesky decomposition and used > it along with BFGS to optimize the likelihood function. I have implemented > the "unrelated" method in Julia and would love to be able to implement this > family based method in Julia as well. >
Ana and I are familiar with using pedigree information in mixed-effects models; we wrote the R package pedigreemm and I am one of the authors of the lme4 package for R. The purpose of creating tools for pedigrees in Julia is to use Pedigrees and MixedModels to fit such models using Julia. I should look again at the kinship package for R. (I get twitchy every time I start to read it because Terry chose to reimplement sparse matrix methods from scratch instead of using the recommended Matrix package for R that Martin MÓ“chler and I wrote). I have the suspicion that the ideas are the same, it's just the names that are different. On Tuesday, December 16, 2014 10:03:06 AM UTC-7, Douglas Bates wrote: >> >> Is anyone working on a Julia package or packages to work with pedigrees, >> in the sense used in animal breeding? Ana Vazquez and I are developing >> such a package which we plan to call Pedigrees. Its principle type will be >> Pedigree, which is constructed from two Integer vectors representing the >> 'sire' and 'dam' of each animal. These names reflect the animal breeding >> orientation of the package. >> >> Capabilities include sorting a pedigree so that parents occur before >> offspring and deriving the additive relationship matrix and other >> quantities related to it, such as inbreeding coefficients. >> >> Is using the name Pedigrees going to cause conflicts? >> >
