I am trying to use the function of fitTimeSeries of metagenomeSeq package.  my dataset are longitudinal dataset of patients. There are multiple data points for each patient

If I use fitTimeSeries to one particular genus, it works. e.g.

res = fitTimeSeries(obj=obj,feature="k__Bacteria:p__Firmicutes:c__Clostridia:o__Clostridiales:f__Lachnospiraceae:g__Dorea",class="type",id="patient",time="ime",B=10)

However, when I try to apply to other genera. it failed with error " invalid 'times’ argument"

timeSeriesFits = lapply(classes,function(i){
        fitTimeSeries(obj=obj,
          feature=i,
            class="type",
            id="patient",
            time="time",
            B=100) 
    })

Could anyone give a hint?

Looking at your particular data, the issue is that you can not have the same ID for samples belonging to both classes. You would have to create a separate ID for the ones in one class and ones for the other class or choose one class for the samples.

Thank you,