[R-sig-eco] Partially non-independent ANOVA?

Chris Howden chris at trickysolutions.com.au
Mon Jun 27 07:01:06 CEST 2011

Hi Mike,

I'm rather new to mixed models, but am on a few lists at the moment to try
and get my head around them. Your comments on using GLMM's on data with
unequal variances gave me a very pleasant surprise! And after thinking
about it I realised it was a fairly obvious use of GLMM's.

Can I just confirm your comments though?

If I was testing some factor that I knew each group had unequal variances
could I test it using something like the following?

lmer(response~factor + (1|factor), data=data)?

Chris Howden
Founding Partner
Tricky Solutions
Tricky Solutions 4 Tricky Problems
Evidence Based Strategic Development, IP Commercialisation and Innovation,
Data Analysis, Modelling and Training
(mobile) 0410 689 945
(fax / office)
chris at trickysolutions.com.au

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-----Original Message-----
From: r-sig-ecology-bounces at r-project.org
[mailto:r-sig-ecology-bounces at r-project.org] On Behalf Of Dunbar, Michael
Sent: Thursday, 23 June 2011 10:59 PM
To: Cliff Beall; r-sig-ecology at r-project.org
Subject: Re: [R-sig-eco] Partially non-independent ANOVA?

Dear Cliff

Using a mixed-effects model (also variously termed multilevel or
hierarchical model) could well be what you are looking for. These are
implemented in several R packages.

In your study, in mixed model parlance, patient identifier would be a
random effect (you don't say how many patients), with some patients having
one measurement and some two, and treatment (control or periodontitis)
would be a fixed effect. How or whether you code the sites (which would be
another fixed effect) depends on whether they are of interest.

These approaches are very powerful, but I wouldn't advise just dipping
into them - it can be hard to get things set up correctly if you just want
"a test", they repay careful study. On the bonus side, once you're
familiar with them you start seeing the everything in a hierarchical

You can model unequal variances by group, although you need to be careful
in model specification.


-----Original Message-----
From: r-sig-ecology-bounces at r-project.org
[mailto:r-sig-ecology-bounces at r-project.org] On Behalf Of Cliff Beall
Sent: 22 June 2011 17:18
To: r-sig-ecology at r-project.org
Subject: [R-sig-eco] Partially non-independent ANOVA?

Dear group-

I was wondering if someone could point me towards the correct statistical
test and R-function for my situation.

I am looking at oral bacteria and have three groups of samples, one from
control subjects, and two that are derived from different sites in
patients with periodontitis. So I have one totally independent group, and
two that have samples that are paired.

I would like to do a test just to say that there are differences between
the three groups, something like an ANOVA, but that deals with the lack of
independence of the two groups.

By the way, for what I am measuring it looks like normality is a
reasonable assumption but equal variances are probably not.


Cliff Beall
Research Assistant Professor
Division of Oral Biology
College of Dentistry
The Ohio State University
beall.3 at osu.edu

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