Entering edit mode

2.7 years ago

Sarah
•
0

Hi,

We analysed the bacterial composition of 10 stool samples (10 different patients; proportion values for the bacterial species) across 3 time points. I would now like to know if there is a trend for any of the detected bacteria to decrease/increase over time.

What statistical test can I use for it? I spent quite some time searching for an appropriate test. The typical tests that are used in ecology research don't allow multiples measurements for the same time point.

Thanks a lot for your help, very much appreciated!

Best wishes, Sarah

Since you have count data, I think a good place to start would be a negative binomial regression. Since you want to know whether there are different trends for different bacteria over time, you would ultimately want an interaction term in your model, such as

`count ~ time:bacteria`

. Depending on how many observations you have per factor level, you could control for differences in patients with a model such as`count ~ patient + time:bacteria`

.Edit: If you want to stick with proportions (which I suggest against if you have the actual count values), you can use a beta regression instead of negative binomial.

I second @rpolicastro answer regarding

`negative binomial`

. Also suggest`generalized mixed models`

for the differences in patients. You can model the heterogeneity as a random effect in your model.