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).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).
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"
)
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"
)
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.
# 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'
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'
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).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")))
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)
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)
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).make_linelist(allow_extra = TRUE)) no longer causes an error (#65, @Bisaloo;
reported by @TimTaylor in #63)This is the first proof-of-concept release on CRAN.
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