Incorporate syntax updates

[alicecima]

The name/structure of some functions in the epi libraries seem to have changed, so parts of the tooling book's code do not currently work.

In general:

• Change covidcast() to pub_covidcast(), and adjust arguments.
• Change pivot_quantiles to pivot_quantiles_wider.
• Change levels to quantile_levels in arx_args_list.
• Change probs to quantile_levels in layer_residual_quantiles, and flatline_args_list.
• Change tau to quantile_levels in quantile_reg.

Chapter 2:

• At line get
  #Warning messages:
  1: epi_archive constructor argument geo_type is now ignored. Consider removing.
  2: epi_archive constructor argument time_type is now ignored. Consider removing.

Chapter 6:

• Error because NULL is not accepted anymore for seasonal_period
• Error with unnest(outlier_info)

Chapter 7:

• Error because archive_cases_dv_subset_dt does not exist

[dshemetov]

Thanks for this comprehensive list Alice! I know that some of these changes have been addressed in #12 (it's been a while, but I recall addressing covidcast() -> pub_covidcast() at least), but we just haven't gotten around to merging that in. We should probably merge that PR in and open a new one for the rest of your checklist (I don't think #12 needs to be re-reviewed). @brookslogan for visibility.

[dshemetov]

closed by #17