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linelist 0.0.2

New features

  • 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")))
  • 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. If you were using this function, we now recommend using the more explicit two-steps process:

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

  • 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)

linelist 0.0.1

CRAN release: 2022-05-13

This is the first proof-of-concept release on CRAN.

New features

  • the linelist class implements a tagging system to keep track of key epidemiological variables in a data.frame

  • validation routines for tagged variables

  • accessors to retrieve tagged variables

  • an API for easy extension to additional tagged variables

  • dedicated S3 methods providing safeguards for operations which could lose tagged variables

  • full documentation of all functions

  • a vignette

  • 100% test coverage