[R] Help to inputting a pre-defined correlation structure in a Mixed Model

albertwschulthess awschult at uc.cl
Tue Nov 22 21:20:09 CET 2011

I'm working in a Gen/Marker-Phenotype association study in wheat and I'm
using a Mixed Model Approach to estimate the effect of the markers. My model
has the atribute measured as y (response variable), the markers and the
blocks (of a complete random block design) as fixed and the genotypes and
the residuals as random. In one hand I'm assuming that there is no
correlation between residuals and that they have a normal distribution with
mean equals to zero and a common variance equals to (sigma e)^2. On the
other hand I'm also asumming that the genotypes are normally distributed
with mean equals to zero but with variance equals to a G matrix that
considers the relatdness between individuals. This G matrix is expressed as
2 * (sigma g)^2 * K, where K is a matrix with the reladness coefficients
(kinship) between all individuals in the study. The K matrix is calculated
outside of R environment, and I'm using it as an input. I'm using the lme
function of the nlme library in R, but I want to know how can I gap the
structures that R offers me (as corrAR1, corrSumm, etc.) as default
structures, because I already have this structure and I only have to
estimate the (sigma g)^2 parameter, possibly using REML. I'm new in the use
of mixed models and I will be very pleased if someone could help me with
this particular question. Thanks a lot in advance. 

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