Changelog • linelist

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 %>%
  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)
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