skimr and write XLSX Enhancements

[rsh52]

Description

This PR seeks to expand on and improve the add_skimr_metadata() and write_redcap_xlsx() functions, reorganize some of the code base, and add new tests to the testthat suite.

Two of the biggest changes involve adding labels to the default skimmers and their output in the Excel sheet and ensuring labels get applied regardless of whether a user executes make_labelled() or add_skimr_metadata() first.

Proposed Changes

List changes below in bullet format:

• Add forwards and backwards compatibility/communication between add_skimr_metadata() and make_labelled()
• Add default skimr labels to XLSX outputs using make_skimr_labs()
• Add the following functions to utils.R, write internal documentation, add tests:
  • is_labelled()
  • make_skimr_labs()
  • safe_set_variable_labels()
• Include redcap_form_label in write_redcap_xlsx() "REDCap Metadata" Sheet output
• Add integration/snapshot test confirming expected output for combined use of make_labelled()/add_skimr_metadata()/write_redcap_xlsx()

Not addressed in this PR

Additional documentation improvements and updates to the README, vignettes, etc. To be included in a subsequent PR once merged.

Issue Addressed

Closes #150

PR Checklist

Before submitting this PR, please check and verify below that the submission meets the below criteria:

• [x] New/revised functions have associated tests
• [x] New/revised functions that update downstream outputs have associated static testing files (.RDS) updated under inst/testdata/create_test_data.R
• [x] New tests that make API calls use httptest::with_mock_api and any new mocks were added to tests/testthat/fixtures/create_httptest_mocks.R
• [x] New/revised functions use appropriate naming conventions
• [x] New/revised functions don't repeat code
• [F] Code changes are less than 250 lines total
• [x] Issues linked to the PR using GitHub's list of keywords
• [x] The appropriate reviewer is assigned to the PR
• [x] The appropriate developers are assigned to the PR
• [x] Pre-release package version incremented using usethis::use_dev_version()

Code Review

This section to be used by the reviewer and developers during Code Review after PR submission

Code Review Checklist

• [ ] I checked that new files follow naming conventions and are in the right place
• [ ] I checked that documentation is complete, clear, and without typos
• [ ] I added/edited comments to explain "why" not "how"
• [ ] I checked that all new variable and function names follow naming conventions
• [ ] I checked that new tests have been written for key business logic and/or bugs that this PR fixes
• [ ] I checked that new tests address important edge cases

[rsh52]

@skadauke skimr manual labels from this morning applied, basically just super simplifies the make_skimr_labels() function.

For the snapshot testing, I tried forcing the example from the expect_snapshot_file() documentation, but couldn't get it to successfully compare the XLSX output in the snaps folder. Defaulting back to this line from the docs:

"Whole file snapshot testing is designed for testing objects that don't have a convenient textual representation, with initial support for images (.png, .jpg, .svg), data frames (.csv), and text files (.R, .txt, .json, ...)"

Instead, went through all of the wb objects and moved the ones of interest to a list() for a single snapshot test.

[skadauke]

Aaaah yes. Codecov 🙂

How about a test that checks that the function returns a named list?

S

---

From: Rich Hanna @.> Sent: Wednesday, May 24, 2023 9:10 AM To: CHOP-CGTInformatics/REDCapTidieR @.> Cc: Stephan Kadauke @.>; Mention @.> Subject: [External]Re: [CHOP-CGTInformatics/REDCapTidieR] skimr and write XLSX Enhancements (PR #151)

@rsh52 commented on this pull request.

---

In tests/testthat/test-utils.Rhttps://github.com/CHOP-CGTInformatics/REDCapTidieR/pull/151#discussion_r1204106390:

• df <- tibble::tribble(
• ~"one", ~"two", ~"three",
• 1, 2, 3
• )
• is_labelled <- is_labelled(df)
• expect_false(is_labelled)
• labels <- c("One", "Two", "Three")
• labelled::var_label(df) <- labels
• is_labelled <- is_labelled(df)
• expect_true(is_labelled) +})

• +test_that("make_skimr_labels works", {

Yea, let's get rid of it. I was thinking more of how I didn't want to see our codecov badge take a hit haha.

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[skadauke]

❤️

---

From: Rich Hanna @.> Sent: Wednesday, May 24, 2023 9:17 AM To: CHOP-CGTInformatics/REDCapTidieR @.> Cc: Stephan Kadauke @.>; Mention @.> Subject: [External]Re: [CHOP-CGTInformatics/REDCapTidieR] skimr and write XLSX Enhancements (PR #151)

@rsh52 commented on this pull request.

---

In tests/testthat/test-utils.Rhttps://github.com/CHOP-CGTInformatics/REDCapTidieR/pull/151#discussion_r1204120437:

• df <- tibble::tribble(
• ~"one", ~"two", ~"three",
• 1, 2, 3
• )
• is_labelled <- is_labelled(df)
• expect_false(is_labelled)
• labels <- c("One", "Two", "Three")
• labelled::var_label(df) <- labels
• is_labelled <- is_labelled(df)
• expect_true(is_labelled) +})

• +test_that("make_skimr_labels works", {

Aaaah yes. Codecov 🙂 How about a test that checks that the function returns a named list?

Sure sounds good to me! Gotta keep the number high and shiny

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[rsh52]

@skadauke changes implemented, emailed over a copy of the labelled skimr XLSX output. 🤞

[rsh52]

Approval secured via e-mail 🚀