*Murtaugh, P.A.* 2007. Simplicity and complexity in ecological data
analysis. *Ecology* 88: 56-62.

is the paper Prof. Bolker referred to.




> depending how you coded population the above is fine. If your have, for
> instance, type : A, B, C, then populations coded as 1,2,3 in each type, the
> syntax above will NOT work.
>
>

Good point, this is correct, you need to have your populations uniquely
labeled otherwise the function cannot tell that pop1 of typeA is distinct
from pop1 of typeB.



> BUT
>
> If you have type A, B, C, then population as 1,2,3,4,5,6 (ideally
> as.factor(population)), or as A1, A2, A3, B1, B2...C3, the syntax above will
> work as if by magic, because I have tried it many times and lme --and lmer I
> presume, is smart enought to see that since population A1 is only found in
> conjunction with type A, population is nested in type.



This is not entirely correct. The syntax will work because the populations
are uniquely labeled but it does not model population as nested within type.
It models there being 12 populations (4 for each of the three types).

These two models are not the same:

lme(growth ~ type, random = ~ 1 | population) - with populations uniquely
identified (A1, A2 ... B1) is not the same as

lme(growth ~ type, random = ~ 1 | type/population) - with populations
"nested" within type



Andy.

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