[R] lmer: random factor nested in a fixed factor

Christian Ritz ritz at life.ku.dk
Mon Oct 6 17:02:08 CEST 2008

Dear Agnes,

I think your model specification should look like this:

YourModel1 <- lmerlmer(y ~ poptype*matingtype + (1|poptype:pop) + (1|poptype:fam),
data = ...)

The "1" in front of "|" refers to models that are random intercepts models as opposed to
general random coefficients models in which case "1" would need to be replaced by a
variable that is quantitative. So, the "(poptype|/pop/fam)" construction is definitely not
relevant to your problem, unless "poptype" is a quantitative variable...

The combined factor "poptype:pop" corresponds to the factor pop, but taking the nesting
structure into account. Similar for the construction "poptype:fam".

>From the summary output of the lmer() fit you should be able to check whether or not the
correct number of groups are used for these random factors.

Kind regards

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