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

Thierry Onkelinx thierry.onkelinx at inbo.be
Tue Mar 20 13:22:34 CET 2018

Dear Vincent,

A mixed model with subject as random intercept is recommended. You need to
think about the counts. Are they really counts? Or are they an ordinal
factor? The negative binomial distribution is OK in case of counts.

GEE is valid in case you want the estimate the marginal effects. Use lme4
or similar when you want conditional effects.

Best regards,

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkelinx at inbo.be
Havenlaan 88 bus 73, 1000 Brussel

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey


2018-03-20 6:58 GMT+01:00 VINCENT KOPPELMANS <vincent.koppelmans at utah.edu>:

> 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
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