Extend xportr_write to accept metadata and deprecate label

[vedhav]

Changes Description

The xportr_write() function follows the same design as the rest of the xportr_* functions by asking for the metadata argument. Thus we're deprecating the label argument from this function.

Setting the dataset label can be done either using xportr_write() or xportr_df_label()

Here is some code to test the xportr_write()

devtools::load_all()

metadata <- data.frame(
  dataset = c("adsl", "adae"),
  label = c("Subject-Level Analysis", "Adverse Events Analysis")
)
adsl <- data.frame(
  USUBJID = c(1001, 1002, 1003),
  SITEID = c(001, 002, 003),
  AGE = c(63, 35, 27),
  SEX = c("M", "F", "M")
)

# Writing with no metadata preset and no metadata passed to `xportr_write()`
adsl |>
  xportr_write(
    path = paste0("nono.xpt"),
    strict_checks = TRUE
  )

# Writing with no metadata preset and passing `label` to `xportr_write()` which will be deprecated
adsl |>
  xportr_write(
    path = paste0("noyes1.xpt"),
    strict_checks = TRUE,
    label = "Subject-Level Analysis"
  )
# Writing with no metadata preset and passing `metadata` to `xportr_write()`
adsl |>
  xportr_write(
    path = paste0("noyes2.xpt"),
    strict_checks = TRUE,
    metadata = metadata
  )

adsl <- xportr_df_label(adsl, metadata)
# Writing with metadata preset and no metadata passed to `xportr_write()`
adsl |>
  xportr_write(
    path = paste0("yesno.xpt"),
    strict_checks = TRUE
  )


# Writing with metadata preset and passing `label` to `xportr_write()` which will be deprecated
adsl |>
  xportr_write(
    path = paste0("yesyes1.xpt"),
    strict_checks = TRUE,
    label = "Subject-Level Analysis"
  )
# Writing with metadata preset and passing `metadata` to `xportr_write()`
adsl |>
  xportr_write(
    path = paste0("yesyes2.xpt"),
    strict_checks = TRUE,
    metadata = metadata
  )

nono <- read_xpt("nono.xpt")
noyes1 <- read_xpt("noyes1.xpt")
noyes2 <- read_xpt("noyes2.xpt")
yesno <- read_xpt("yesno.xpt")
yesyes1 <- read_xpt("yesyes1.xpt")
yesyes2 <- read_xpt("yesyes2.xpt")

attr(nono, "label")
# NULL
attr(noyes1, "label")
# [1] "Subject-Level Analysis"
attr(noyes2, "label")
# [1] "Subject-Level Analysis"
attr(yesno, "label")
# [1] "Subject-Level Analysis"
attr(yesyes1, "label")
# [1] "Subject-Level Analysis"
attr(yesyes2, "label")
# [1] "Subject-Level Analysis"

Task List

• The spirit of xportr is met in your Pull Request
• Place Closes Site examples not using xportr_df_label() #179 into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update)
• Summary of changes filled out in the above Changes Description. Can be removed or left blank if changes are minor/self-explanatory.
• Check that your Pull Request is targeting the devel branch, Pull Requests to main should use the Release Pull Request Template
• Code is formatted according to the tidyverse style guide. Use styler package and functions to style files accordingly.
• Updated relevant unit tests or have written new unit tests. See our Wiki for conventions used in this package. Still at 100% ;) But need to update the tests.
• Creation/updated relevant roxygen headers and examples. See our Wiki for conventions used in this package.
• Run devtools::document() so all .Rd files in the man folder and the NAMESPACE file in the project root are updated appropriately
• Run pkgdown::build_site() and check that all affected examples are displayed correctly and that all new/updated functions occur on the "Reference" page.
• Update NEWS.md if the changes pertain to a user-facing function (i.e. it has an @export tag) or documentation aimed at users (rather than developers)
• Address any updates needed for vignettes and/or templates
• Link the issue Development Panel so that it closes after successful merging.
• Fix merge conflicts
• Pat yourself on the back for a job well done! Much love to your accomplishment!

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (9725e9a) 100.00% compared to head (3d90cd0) 100.00%.
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@@            Coverage Diff            @@
##              main      #185   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           12        12           
  Lines          581       588    +7     
=========================================
+ Hits           581       588    +7     

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[elimillera]

A couple small doc comments but looks great

[bms63]

I think I just have concerns on the documentation when we don't use xportr_metadata() to set everything for the dataset label.

[vedhav]

Not sure if I went overboard by exporting the dataset_spec so asking for a re-review. Perhaps just reading it from the path system.file(paste0("specs/", "ADaM_admiral_spec.xlsx"), package = "xportr") could have been okay, like we do in the README.md What are your thoughts?