[R] Help with Subtracting an effect from a Mixed Model

From: Matthew Forister <forister_at_life.bio.sunysb.edu>
Date: Mon 31 Oct 2005 - 03:02:31 EST

Hi Everyone,

I posted a similar question about a week ago, but haven't gotten any replies -- I'm afraid that's because my previous question was too vague. Let me try again with a more specific question, and I hope someone can help. NOTE, I know I should be using the newer lme4 package, I just haven't had a chance to update my version of R yet, so the question below relates to nmle.

I have data from a classical quantitative genetics experiment, with 33 sires mated each to 2 dams, with 15 progeny from each dam raised on 5 host plants (3 larvae per host). So the model I would like to run has the following factors:
Host (fixed)
Sire (random)
Dam [nested within sire] (random)
Host * Sire (random interaction)
Host * Dam [nested within sire] (random interaction)

This is the code I am using for that complete model: lme1=lme(gain~host,random=~host|sire/dam) I would like to try the model with and without each of those random interactions (host*sire and host*dam-nested-within-sire).

WHAT IS THE SYNTAX FOR SUBTRACTING AN EFFECT FROM THE RANDOM STATEMENT? I have tried:
lme1=lme(gain~host,random=~host|sire/dam-sire:host) But I get an "Invalid formula for groups" error. Alternatively, I tried reorganizing the code, so that the interaction would be left out. But there is no way to take out host*sire while still leaving in host*dam nested within sire.

any help will be greatly appreciated!
Matt


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