linelist v1.0.0

We are very excited to announce the release of a new linelist version v1.0.0. Here is a automatically generated summary of the changes in this version.

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 (@dgmascarina)

• 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 (#76, @Bisaloo)
• testthat tests now warn on partial matching (#76, @Bisaloo)