epiprocess 0.6.0

Breaking changes

• Changes to both epi_slide and epix_slide
  • The n, align, and before arguments have been replaced by new
    before and after arguments. To migrate to the new version, replace
    these arguments in every epi_slide and epix_slide call. If you were
    only using the n argument, then this means replacing n = <n value>
    with before = <n value> - 1.
  • epi_slide's time windows now extend before time steps before and
    after time steps after the corresponding ref_time_values. See
    ?epi_slide for details on matching old alignments.
  • epix_slide's time windows now extend before time steps before the
    corresponding ref_time_values all the way through the latest data
    available at the corresponding ref_time_values.
  • Slide functions now keep any grouping of x in their results, like
    mutate and group_modify.
    • To obtain the old behavior, dplyr::ungroup the slide results immediately.
• Additional epi_slide changes:
  • When using as_list_col = TRUE together with ref_time_values and
    all_rows=TRUE, the marker for excluded computations is now a NULL entry
    in the list column, rather than a NA; if you are using tidyr::unnest()
    afterward and want to keep these missing data markers, you will need to
    replace the NULL entries with NAs. Skipped computations are now more
    uniformly detectable using vctrs methods.
• Additionalepix_slide changes:
  • epix_slide's group_by argument has been replaced by dplyr::group_by and
    dplyr::ungroup S3 methods. The group_by method uses "data masking" (also
    referred to as "tidy evaluation") rather than "tidy selection".
    • Old syntax:
      • x %>% epix_slide(<other args>, group_by=c(col1, col2))
      • x %>% epix_slide(<other args>, group_by=all_of(colname_vector))
    • New syntax:
      • x %>% group_by(col1, col2) %>% epix_slide(<other args>)
      • x %>% group_by(across(all_of(colname_vector))) %>% epix_slide(<other args>)
  • epix_slide no longer defaults to grouping by non-time_value, non-version
    key columns, instead considering all data to be in one big group.
    • To obtain the old behavior, precede each epix_slide call lacking a
      group_by argument with an appropriate group_by call.
  • epix_slide now guesses ref_time_values to be a regularly spaced sequence
    covering all the DT$version values and the version_end, rather than the
    distinct DT$time_values. To obtain the old behavior, pass in
    ref_time_values = unique(<ungrouped archive>$DT$time_value).
• epi_archive's clobberable_versions_start's default is now NA, so there
  will be no warnings by default about potential nonreproducibility. To obtain
  the old behavior, pass in clobberable_versions_start = max_version_with_row_in(x).

Potentially-breaking changes

• Fixed [ on grouped epi_dfs to maintain the grouping if possible when
  dropping the epi_df class (e.g., when removing the time_value column).
• Fixed epi_df operations to be more consistent about decaying into
  non-epi_dfs when the result of the operation doesn't make sense as an
  epi_df (e.g., when removing the time_value column).
• Changed bind_rows on grouped epi_dfs to not drop the epi_df class. Like
  with ungrouped epi_dfs, the metadata of the result is still simply taken
  from the first result, and may be inappropriate
  (#242).
• epi_slide and epix_slide now raise an error rather than silently filtering
  out ref_time_values that don't meet their expectations.

New features

• epix_slide, <epi_archive>$slide have a new parameter all_versions. With
  all_versions=TRUE, epix_slide will pass a filtered epi_archive to each
  computation rather than an epi_df snapshot. This enables, e.g., performing
  pseudoprospective forecasts with a revision-aware forecaster using nested
  epix_slide operations.

Improvements

• Added dplyr::group_by and dplyr::ungroup S3 methods for epi_archive
  objects, plus corresponding $group_by and $ungroup R6 methods. The
  group_by implementation supports the .add and .drop arguments, and
  ungroup supports partial ungrouping with ....
• as_epi_archive, epi_archive$new now perform checks for the key uniqueness
  requirement (part of
  #154).

Cleanup

• Added a NEWS.md file to track changes to the package.
• Implemented ?dplyr::dplyr_extending for epi_dfs
  (#223).
• Fixed various small documentation issues (#217).

Full Changelog: https://github.com/cmu-delphi/epiprocess/commits/v0.6.0