[R-sig-ME] Repeated-measures analysis with count data following a negative-binomial distribution

Paul Johnson paul.johnson at glasgow.ac.uk
Tue Mar 20 17:56:06 CET 2018

Just on the GEE vs GLMM question, this is a really nice clear article explaining the differences and how to choose:

Marginal or conditional regression models for correlated non‐normal data?
Muff et al. 2016 MEE.

Remarkably it has been cited only once in 2 years (Google Scholar).

To summarise their recommendations: in most cases you'll want a conditional (GLMM) model.

> On 20 Mar 2018, at 05:58, VINCENT KOPPELMANS <vincent.koppelmans at utah.edu> wrote:
> Dear all,
> I am looking for advice on how to run a repeated analysis on count data.
> My issue is as follows:
>  *   We counted the number of carotid plaques from ultrasound images in a diseased population and a group of control subjects
>  *   We have measured the plaques for all subjects in both the left and the right carotid artery during the same session
>  *   The number of plaques is a count score ranging from 0 to 6
>  *   The distributions look like this:
>     *   Plaques in the left carotid artery: https://www.dropbox.com/s/t5tqh4wjrfc5eml/Left.png?dl=0
>     *   Plaques in the right carotid artery: https://www.dropbox.com/s/nl5ezef145av2ae/Right.png?dl=0
>     *   (Where NKI= the diseased population; RSS= the control subjects; (all)= the two groups combined. There are no numbers on the x-axis, but the 7 columns are the count scores 0-6 (left to right).)
>  *   There is biological evidence that the distribution of plaques for left and right differ in the general population (i.e., our control subjects).
>  *   I would like to test if the difference in distribution of plaque scores between the left and right carotid arteries is different between my two populations.
>  *   Previous analyses (e.g., comparing a single side between groups) showed me that a negative binomial distribution is a better fit for my data than a Poisson distribution.
> My idea is to run a repeated-measures negative binomial regression analysis where plaque score measures (left and right) would be the repeated measures. In this case I would be interested in the �body side� by group interaction.
> My questions are:
>  *   Is a good and valid approach?
>  *   I am thinking about using R�s GEE package (https://cran.r-project.org/web/packages/gee/index.html). Would that be the right tool for this job?
> Thanks!
> - Vincent
> 	[[alternative HTML version deleted]]
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