Running songbird for differential abundance analysis and the variable of interest is a categorical variable with the following labels: healthy controls, untreated, 1 month treatment, and 6 months treatment. I’ve been trying to create a model using songbird to see which microbes are changing from each group but so far my models are relatively poor performing, and I am unable to get loss to decrease and for the R-squared to increase.
I was wondering if I could just somehow specify in the model formula to only compare the healthy controls and untreated, to see if the model can at least discriminate that. That is the major comparison I am interested in, but I don’t know how to specify in the formula to just ignore the treatment groups. Judging from our other data, I’m worried that the treated groups look too similar to the healthy controls which is leading to the poor model performance. Any help in designing a formula or other comparison ideas would be appreciated!