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I have ordinal data from two groups over time. I want to know the if the data are different between the two groups at each time point. I know it should be a non-parametric test but am not sure how to get the multiple comparisons that I want. Currently using Graphpad prism for analysis although I can also use R.

Thanks!

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As far as I know this is not possible in GraphPad Prism.

There are some software packages in R that are designed to handle this type of modeling where you want to use a random effect to account for longitudinal sampling and your response is ordinal.

Check out the mixor R package. The vignette includes an example of longitudinal data.

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