Hello,
I have two very rudimentary questions regarding the random effects terms
in the lme and lmer functions. I apologize if this also partly strays
into a general statistics question, but I'm a bit new to this all. So
hopefully it'll be a quick problem to sort out...
Here is my experimental setup: I raised butterflies in 5 different
testing chambers all set to different temperatures. Within the testing
chambers, the butterflies were held in 10 different sleeves, which were
rotated daily to compensate for microenvironmental effects. I measured
several traits of the butterflies and I am constructing models for each
trait (unfortunately, multivariate analysis isn't possible). In my
models, sex and temperature are fixed factors and the sleeve is a random
effect. Most of the response variables are normally distributed, but
there is one with a Gamma distribution (time until an event) and another
with poisson distribution (counts), so some models use lme while others
use lmer. I would like to determine if, despite the daily rotation,
there are still random effects from the individual sleeves. My two
questions (assuming I haven't already made grave errors in my
description of the setup) are:
1) In my data file, the "sleeve" variable is just marked with a number 1
through 10; the temperature is noted in a different column, so the 50
sleeves do not have unique names, but rather there are 5 instances of
each of the 10 sleeve numbers. If sleeve is to be properly included in
the models as a random effect, is it sufficient to leave the values as
they are or should I generate unique names for all combinations of
sleeve number and temperature, using something like
> data$sleeve.in.temp <- factor(with(data, temp:sleeve)[drop=TRUE])
2) (this is the one that strays more into standard statistics territory,
sorry) I'm a bit confused on how to actually set up the random effects
term for the models. Given my experimental setup, using the lme syntax,
should it be:
> model <- lme(response ~ sex*temp, random=~temp|sleeve, data)
or
> model <- lme(response ~ sex*temp, random=~1|sleeve, data)
or something else? I've searched and searched, but everything I find
online seems to be significantly more advanced than what I'm doing,
leaving me even more confused than when I started!
Thank you very much for your help!! I want to be sure I do this analysis
right....
Cheers,
-brandon
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