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

Dunbar, Michael J. mdu at ceh.ac.uk
Thu Jun 23 14:59:01 CEST 2011

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 mindset!

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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