Changelog • linelist

linelist 2.0.0

Breaking changes

Deprecated functions and arguments have been completely removed. The following operations are no longer possible:

List of tags now needs to be spliced in make_linelist():

my_tags <- list(
  id = "case_ID",
  date_onset = "date_of_prodrome",
  age = "age",
  gender = "gender"
)

# No longer possible
make_linelist(obj, my_tags)

# Instead slice list in dynamic dots
make_linelist(obj, !!!my_tags)

select_tags():

# No longer possible
x %>%
  select_tags("age")

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

select.linelist(). This change should be invisible to users since the parent method select.data.frame() will be used with the same effect.
lost_tags_action() as part of a pipeline is no longer possible:

# No longer possible
make_linelist(cars, date_onset = "dist", date_outcome = "speed") |>
  lost_tags_action("none") |>
  dplyr::select(-dist)

# Instead do
lost_tags_action("none")
make_linelist(cars, date_onset = "dist", date_outcome = "speed") |>
  dplyr::select(-dist)

linelist 1.1.4

CRAN release: 2024-06-17

Internal change

Promotion of testthat warnings to errors on CI is restored, thanks to a report and suggestion by @krlmlr. This was accidentally removed during #123 (#128).

New features

Default tag loss condition can now permanently be set via an environment variable LINELIST_LOST_ACTION (@Bisaloo, #126). The environment variable needs to be set before the R session is started due to the way R environment variables work. This allow users to set a stricter default behaviour for tag loss if they want to ensure tag loss never go unnoticed (#104).
validate_linelist() now returns invisibly, with a message, for valid linelist object (@Bisaloo, #146, based on a report from @avallecam in #143).

linelist 1.1.3

CRAN release: 2024-04-21

Minor change

Convert meta$Date in CITATION to Date before attempting to run format() (@Bisaloo, #125)

linelist 1.1.2

CRAN release: 2024-04-19

Minor change

Fix URL in CITATION (@Bisaloo, #123)

linelist 1.1.1

Minor change

Tests no longer error on warnings on CRAN, to avoid false positives on a platform where we have limited control (@Bisaloo, #123).

linelist 1.1.0

CRAN release: 2024-02-28

Breaking changes

make_linelist() and set_tags() no longer accept a named list of characters as input. Instead, make_linelist(), set_tags() and tags_types() now use rlang’s dynamic dots, which means that you can splice list arguments. This implementation is more robust, better tested, and makes it explicit that users want to splice the list (@Bisaloo, #96).

Before:

my_tags <- list(
  id = "case_ID",
  date_onset = "date_of_prodrome",
  age = "age",
  gender = "gender"
)
make_linelist(obj, my_tags)
# OR
make_linelist(
  obj,
  id = "case_ID",
  date_onset = "date_of_prodrome",
  age = "age",
  gender = "gender"
)

Now:

my_tags <- list(
  id = "case_ID",
  date_onset = "date_of_prodrome",
  age = "age",
  gender = "gender"
)
make_linelist(obj, !!!my_tags)
# OR
make_linelist(
  obj,
  id = "case_ID",
  date_onset = "date_of_prodrome",
  age = "age",
  gender = "gender"
)

New features

linelist warnings and errors in the case of a tag loss now have a custom class (@Bisaloo, #109), which means it is easier to silence them specifically, or to catch them programmatically for advanced error handling. One example of a new advanced condition handling that was before not possible is:

warning_counter <- 0

withCallingHandlers({
  x <- linelist::make_linelist(cars, date_onset = "dist", age = "speed")
  x <- x[, -1]
  x <- x[, -1]
  warning("This is not a linelist warning", call. = FALSE)
}, linelist_warning = function(w) {
  warning_counter <<- warning_counter + 1
})
#> Warning: The following tags have lost their variable:
#>  age:speed
#> Warning: The following tags have lost their variable:
#>  date_onset:dist
#> Warning: This is not a linelist warning

warning("This pipeline generated ", warning_counter, " linelist warnings.")
#> Warning: This pipeline generated 2 linelist warnings.

linelist objects now have a new custom $<-.linelist() to prevent tag loss when subsetting a linelist object (@Bisaloo, #86). This completes the functionality already provided by the [<-.linelist() and [[<-.linelist() methods.
```
x$tagged_column <- NULL
#> Warning in prune_tags(out, lost_action): The following tags have lost their variable:
#>  tag:tagged_column
```

Validation failures in validate_types() now integrate a delayed error mechanism (@Bisaloo, #106). This ensures that the error message will return all the invalid tag types at once rather than having to go through multiple trials and runs.

Before: only the first invalid tag type is returned.

# No warning about age, even though it also has an invalid type
x <- make_linelist(cars, age = "speed", gender = "dist")
validate_types(x, ref_types = tags_types(age = "factor"))
#> Error in validate_types(x, ref_types = tags_types(age = "factor")) : 
#>   Issue when checking class of tag `gender`:
#> Must inherit from class 'character'/'factor', but has class 'numeric'

Now: the error message returns all the invalid tag types at once.

x <- make_linelist(cars, age = "speed", gender = "dist")
validate_types(x, ref_types = tags_types(age = "factor"))
#> Some tags have the wrong class:
#>   - gender: Must inherit from class 'character'/'factor', but has class 'numeric'
#>   - age: Must inherit from class 'factor', but has class 'numeric'

Internal changes

Internal duplication in the specification of the tags supported by linelist by default has been removed. This makes it easier to add or remove tags in the future, and reduces the risk of inconsistencies between the different parts of the package (@Bisaloo, #111).
The internal tag_variable() function has been replace by a vectorized alternative tag_variable, thus improving performance in make_linelist() and set_tags() about twofold. The error message when tags are specified by position with a number larger than the number of columns in the dataset to tag has also been clarified (@Bisaloo, #110).

Documentation

linelist now provides a design vignette for future contributors or maintainers (@Bisaloo, #112).

linelist 1.0.0

CRAN release: 2023-10-19

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 @dgmascarina contribution
added short lay description to README thanks to Emma Marty’s contribution
fixed some typos in package documentation (@pitmonticone, #30)

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)

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