mixed-effects ordinal logistic regression model

Hi list



I have a dataset with n=60 animals with two groups (30/group; control and
treatment) on 3 different research sites. Animals are monitored on days 0,
14 and 28 (repeated measures), and lesions are scored from 1-4.



I want to use a mixed-effects ordinal logistic regression model and
consider
animals and research sites as random-effects in the model.

I haven't done ordinal logistic regression before, and I would like to use
this data and learn how to do the analysis and also interpret the outputs.
I
appreciate any help on;



1- A book, paper or link on ordinal logistic regression (easy to read and
understand for an average reader)

2- What is the preferred package in R to analyse such data? I noticed some
have used "Ordinal" package.

3- Is it appropriate to use farm (n=3) as a random-effects in the model? I
assume 3 is small to be considered as a random-effects in the model, your
thoughts?

4- Because observations are repeated on 3 occasions (repeated measures), I
intend to use animals as a random-effects.

5- If I use both research sites and animals as random-effects, I assume it
would be a nested random-effects model?

6- I appreciate if someone can help with some R codes on ordinal logistic
regression



Your help is greatly appreciated!



Ahmad










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