linelist 1.0.0

linelist 1.0.0

New features

• Increased compatibility with dplyr is now documented and ensured through
  tests of all dplyr verbs on linelist objects as part of our testing & continuous
  integration system, as well as a new vignette:
  https://epiverse-trace.github.io/linelist/articles/compat-dplyr.html
  (@Bisaloo, #53)

• A new selection helper is provided for tidyverse users, based on the existing
  selectors provided by the tidyselect package: has_tag() (@Bisaloo, #61). By
  feeding it a character vector of tags to operate on, you can work with dplyr
  verbs on specific tagged columns without having to explicitly use the column
  names:

  x %>%
    dplyr::select(has_tag(c("id", "date_of_onset")))

Breaking changes

• It is no longer possible to use lost_tags_action() within a pipeline. It
  must now be set as a separate step. This makes the internal code more robust and
  clarifies what is part of the pipeline versus a global option (@Bisaloo, #79).

• The select_tags() function is now deprecated to ensure we provide just one
  clear way to address a given issue and that our "happy path" is clearly
  signposted (@Bisaloo, #61). If you were using this function, we now recommend
  using the more explicit two-steps process:

  # Deprecated
  x %>%
    select_tags("age")
  
  # Instead use
  x %>%
    tags_df() %>%
    select(age)
  
  # Or
  x %>%
    select(has_tag("age")) %>%
    tags_df()

• The custom select.linelist() method has been deprecated as providing a
  custom [.linelist() is sufficient to ensure compatibility with
  dplyr::select() default methods, including triggering lost_tags_action()
  on tag removal (@Bisaloo, #61).
  A full deletion of this method is not possible at the moment because we want to
  provide a smooth transition for users that relied on the custom tags argument
  of the select.linelist() method. It is now recommend instead to use the new
  has_tag() selection helper:

  x %>%
    dplyr::select(has_tag(c("id", "date_of_onset")))
    
  # Instead of
  x %>%
    select(tags = c("id", "date_of_onset"))

• The custom rename.linelist() method has been removed as providing a custom
  names<-().linelist method is sufficient to ensure compatibility with
  dplyr::rename(), including appropriate modification of the tags. (@Bisaloo,
  #60)

Documentation

• added a hex logo thanks to David Mascarina's contribution

• added short lay description to README thanks to Emma Marty's contribution

Bug fixes

• linelist is now explicitly marked as incompatible with data.table.
  In practice, make_linelist(x) now errors if x inherits from data.table
  (#55, @Bisaloo, based on discussions with @TimTaylor).
• [.linelist() now works to subset by column when including just one argument
  (#54, @Bisaloo). E.g., x[1]. As an indirect effect, this also improves
  compatibility with dplyr verbs that rely on this method (#51).
• subsetting a linelist with extra tags (e.g., created via
  make_linelist(allow_extra = TRUE)) no longer causes an error (#65, @Bisaloo;
  reported by @TimTaylor in #63)

Internal changes

• testthat tests now run in parallel (#77, @Bisaloo)
• testthat tests now warn on partial matching (#77, @Bisaloo)