[R-sig-ME] [R] Meaning of /, :, and %in% in lmer
Claus Wilke
cwilke at mail.utexas.edu
Fri Apr 18 18:47:07 CEST 2008
> The short answer is that (1|A/B) is expanded to (1|A) + (1|A:B) so you
> can choose whatever form makes sense to you.
Thanks, that was what I needed to hear.
>
> There are different circumstances where a notation like (1|A/B) would
> be used. Some are reasonable choices and some are artifacts of
> artificial ways of assigning labels to factor levels. Rather than my
> trying to guess what kind of application you have in mind, could you
> describe a situation where you would want to fit an lmer model with
> terms like that?
It's a virology experiment. We have two ancestral strains. From each of those
we have derived several new strains, and then have made multiple fitness
measurements on the new strains. We want to know whether the ancestral strain
has an effect on the fitness of the derived strains. The model I'm using for
that is
fitness ~ ancestor + (1|ancestor:strain),
because strains are nested within ancestors. If I were using
fitness ~ ancestor + (1|ancestor/strain),
then ancestor would get both a fixed and a random effect, which doesn't make
sense.
I have a second question, related to the hypothesis testing of whether the
fixed ancestor effect is significant. I've read all the threads about why it
is problematic to do an F test to calculate a p value, and that it is better
to do markov-chain monte carlo. My question is: Is there a proper reference I
can cite to substantiate the claim that the standard (i.e., SAS) way of
calculating significance in this case is problematic, or do I have to refer
to the mailing list archive?
Thanks a lot,
Claus
--
Claus Wilke
Section of Integrative Biology
and Center for Computational Biology and Bioinformatics
University of Texas at Austin
1 University Station C0930
Austin, TX 78712
cwilke at mail.utexas.edu
512 471 6028
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