[R-sig-eco] Random or repeated?
Dixon, Philip M [STAT]
pdixon at iastate.edu
Fri Dec 9 18:23:55 CET 2011
Kyle,
The eco-stat list seems the wrong place to ask this question. The people to ask are the quantitative plant breeders, e.g. at Texas A&M.
Some general advice about random effects and correlated observations, for either trait data or ecological data:
1) random effects provide a way to model correlations among errors. So do 'repeated measures'.
2) what matters are the correlations among ERRORS. If I remember the traditional QTL model correctly, errors are independent conditional on the state of the flanking markers. So, you don't need random effects for RIL's, if you're analyzing a single trait at a time. Your observation is correct: the random effect and the marker fixed effects are both trying to model the same thing. The same trait measured in multiple environments is often considered as a multi-trait analysis, to estimate the correlation between pairs of environments. It could also be analyzed as a single trait, with a model that includes fixed effects of environments. Different models answering different questions.
3) yes, pedigrees (or relatedness coefficients) can be used to parameterize a correlation matrix. This provides one way (not the only way) to account for phylogenetic relatedness. Animal breeders use pedigree-based correlation matrices all the time.
Philip Dixon
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