preliminary feedback

[davidchampredon]

After taking a first stab at playing with the package, here are my initial comments :

• remove duplicate title in README
• 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, ...)
• give an example of how we can see the variant matrix used, how we can create/modify one (get_mutation_defs(res))
• 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.
• hide internal functions from the package documentation
• give example that calculates the confidence intervals