This package should only deal with one timepoint. It investigates and analyze the diversity and groupings of the sequences in a single timepoint.
A subsequent package, something like HaplotypeTracker, can import this package and add the time dimension too the things done in this package.
I think this is a reasonable design decision because there are many situations in which you will want to explore haplotypes without having the time dimension in your data.
This package should only deal with one timepoint. It investigates and analyze the diversity and groupings of the sequences in a single timepoint.
A subsequent package, something like HaplotypeTracker, can import this package and add the time dimension too the things done in this package.
I think this is a reasonable design decision because there are many situations in which you will want to explore haplotypes without having the time dimension in your data.