Hierarchical timepoints #2
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Go from collapsed_sequence_counts.tsv to annotated_sequence_counts.tsv. This converts location of "USA" to "USA_2023-24", etc... by appending timepoint
If "other" is the same label across timepoints, estimating a single fitness for "other" will be wonky
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Instead of "scaffolding" across independently run timepoints, instead run a hierarchical model where each timepoint is its own "location", ie
It should be okay that variants don't fully span locations (aka timepoints) in the hierarchical model as long as there is a pivot bridge between locations.
This combines sequence counts from different timepoints into a single aggregated sequence count file. In this aggregation, the "location" field is suffixed by timepoint. Hierarchical MLR is run on the aggregated timepoints.