epiprocess 0.3.0

Breaking changes

• as_epi_archive, epi_archive$new:
  • Compactification (see below) by default may change results if working
    directly with the epi_archive's DT field; to disable, pass in
    compactify=FALSE.
• epi_archive's wrappers and R6 methods have been updated to follow these
  rules regarding reference semantics:
  • epix_<method> will not mutate input epi_archives, but may alias them
    or alias their fields (which should not be a worry if a user sticks to
    these epix_* functions and "regular" R functions with
    copy-on-write-like behavior, avoiding mutating functions [.data.table).
  • x$<method> may mutate x; if it mutates x, it will return x
    invisibly (where this makes sense), and, for each of its fields, may
    either mutate the object to which it refers or reseat the reference (but
    not both); if x$<method> does not mutate x, its result may contain
    aliases to x or its fields.
• epix_merge, <epi_archive>$merge:
  • Removed ..., locf, and nan parameters.
  • Changed the default behavior, which now corresponds to using
    by=key(x$DT) (but demanding that is the same set of column names as
    key(y$DT)), all=TRUE, locf=TRUE, nan=NaN (but with the
    post-filling step fixed to only apply to gaps, and no longer fill over
    NAs originating from x$DT and y$DT).
  • x and y are no longer allowed to share names of non-by columns.
  • epix_merge no longer mutates its x argument (but $merge continues
    to do so).
  • Removed (undocumented) capability of passing a data.table as y.
• epix_slide:
  • Removed inappropriate/misleading n=7 default argument (due to
    reporting latency, n=7 will not yield 7 days of data in a typical
    daily-reporting surveillance data source, as one might have assumed).

New features

• as_epi_archive, epi_archive$new:
  • New compactify parameter allows removal of rows that are redundant for the
    purposes of epi_archive's methods, which use the last version of each
    observation carried forward.
  • New clobberable_versions_start field allows marking a range of versions
    that could be "clobbered" (rewritten without assigning new version
    tags); previously, this was hard-coded as max(<epi_archive>$DT$version).
  • New versions_end field allows marking a range of versions beyond
    max(<epi_archive>$DT$version) that were observed, but contained no
    changes.
• epix_merge, $merge:
  • New sync parameter controls what to do if x and y aren't equally
    up to date (i.e., if x$versions_end and y$versions_end are
    different).
• New function epix_fill_through_version, method
  <epi_archive>$fill_through_version: non-mutating & mutating way to
  ensure that an archive contains versions at least through some
  fill_versions_end, extrapolating according to how if necessary.
• Example archive data object is now constructed on demand from its
  underlying data, so it will be based on the user's version of
  epi_archive rather than an outdated R6 implementation from whenever the
  data object was generated.

Full Changelog: https://github.com/cmu-delphi/epiprocess/commits/v0.3.0