After taking a first stab at playing with the package, here are my initial comments :
[x] remove duplicate title in README
[x] increment version number as needed (this may be helpful especially in this development phase)
[ ] add clear (could be brief) documentation for functions mentioned in the README file (parse_mutations, get_mutation_defs, ...)
[x] give an example of how we can see the variant matrix used, how we can create/modify one (get_mutation_defs(res))
[x] x-axis in autoplot(..., date_col = 'date') gets busy when large number of dates. Consider defaulting to weekly or monthly based on the date range of the data plotted.
[ ] is there a check of the variant matrix if two definitions are equivalent? for example one defining the mutation in terms of nucleotides and the other in terms of AA.
[x] hide internal functions from the package documentation
[x] give example that calculates the confidence intervals
After taking a first stab at playing with the package, here are my initial comments :
READMEparse_mutations,get_mutation_defs, ...)get_mutation_defs(res))autoplot(..., date_col = 'date')gets busy when large number of dates. Consider defaulting to weekly or monthly based on the date range of the data plotted.