[R] nested ANCOVA: still confused
HDoran at air.org
Tue Jan 24 21:04:21 CET 2006
I see the issues in your code and have provided what I think will solve
your problem. It is often much easier to get help on this list when you
provide a small bit of data that can be replicated and you state what
the error messages are that you are receiving. OK, with that said, here
is what I see. First, you do not need to use the syntax bb$sex in your
model, this can be significantly simplified. Second, you do not have a
random statement in your model.
Here is your original model:
lme(bb$rtot~bb$sex, bb$purban|bb$chick/bb$box, na.action=na.omit)
Here is what it should be:
lme(fixed = rtot~sex, random=~purban|chick/box, na.action=na.omit,
Notice there is a fixed and random call. You can simplify this as
lme(rtot~sex, random=~purban|chick/box, na.action=na.omit, bb)
Note, you can eliminate the "fixed=" portion but not the random
Last, if you want to do this in lmer, the newer function for mixed
models in the Matrix package, you would do
lmer(rtot~sex + (purban|box:chick) + (purban|box), na.action=na.omit,
Hope this helps.
From: r-help-bounces at stat.math.ethz.ch
[mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Jeffrey Stratford
Sent: Tuesday, January 24, 2006 11:34 AM
To: r-help at stat.math.ethz.ch
Subject: [R] nested ANCOVA: still confused
I did some more research and I'm still not sure how to set up an ANCOVA
with nestedness. Specifically I'm not sure how to express chicks nested
within boxes. I will be getting Pinheiro & Bates (Mixed Effects Models
in S and S-Plus) but it will not arrive for another two weeks from our
The goal is to determine if there are urbanization (purban) effects on
chick health (rtot) and if there are differences between sexes (sex) and
the effect of being in the same clutch (box).
The model is rtot = sex + purban + (chick)box.
I've loaded the package lme4. And the code I have so far is
bb <- read.csv("C:\\eabl\\eabl_feather04.csv", header=TRUE) bb$sex <-
factor(bb$sex) rtot.lme <- lme(bb$rtot~bb$sex,
but this is not working.
Any suggestions would be greatly appreciated.
Jeffrey A. Stratford, Ph.D.
331 Funchess Hall
Department of Biological Sciences
Auburn, AL 36849
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