forest plot rework

[Melkiades]

What changes are proposed in this pull request?

• Complete rework of forest plot function (add_forest()) as attached ggplot2 for each row.
• Removed g_forest() and its dependencies.

Provide more detail here as needed.
#160

# Simple example ------------------------------------------------------------
trial |>
  select(age, marker, grade, response) |>
  tbl_uvregression(
    y = response,
    method = glm,
    method.args = list(family = binomial),
    exponentiate = TRUE,
    hide_n = TRUE
  ) |>
  modify_column_merge(
    pattern = "{estimate} (95% CI {ci}; {p.value})",
    rows = !is.na(estimate)
  ) |>
  modify_header(estimate = "**Odds Ratio**") |>
  add_forest(table_engine = "gt")

# Realistic example ---------------------------------------------------------
trial |>
  tbl_roche_subgroups(
    rsp = "response",
    by = "trt",
    subgroups = c("grade", "stage"),
    ~ glm(response ~ trt, data = .x) |>
      gtsummary::tbl_regression(
        show_single_row = trt,
        exponentiate = TRUE
      )
  ) |>
  add_forest(pvalue = starts_with("p.value"), table_engine = "flextable")

New generic format (inspired by gtforester @ddsjoberg)

More specific output:

---

Pre-review Checklist (if item does not apply, mark is as complete)

• All GitHub Action workflows pass with a ✅
• PR branch has pulled the most recent updates from master branch: usethis::pr_merge_main()
• If a bug was fixed, a unit test was added.
• Code coverage is suitable for any new functions/features (generally, 100% coverage for new code): devtools::test_coverage()
• Request a reviewer

Reviewer Checklist (if item does not apply, mark is as complete)

• If a bug was fixed, a unit test was added.
• Run pkgdown::build_site(). Check the R console for errors, and review the rendered website.
• Code coverage is suitable for any new functions/features: devtools::test_coverage()

When the branch is ready to be merged:

• Update NEWS.md with the changes from this pull request under the heading "# cards (development version)". If there is an issue associated with the pull request, reference it in parentheses at the end update (see NEWS.md for examples).
• All GitHub Action workflows pass with a ✅
• Approve Pull Request
• Merge the PR. Please use "Squash and merge" or "Rebase and merge".

[Melkiades]

@shajoezhu @BFalquet let me know what you think! I managed to get also the flextable output to work with our theme

[github-actions]

Unit Tests Summary

  1 files   77 suites   1m 52s ⏱️
 77 tests  77 ✅ 0 💤 0 ❌
197 runs  197 ✅ 0 💤 0 ❌

Results for commit f018e93.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
add_forest	👶		$+0.00$	$+5$	$0$	$0$	$0$
forestplot	💀	$0.04$	$-0.04$	$-1$	$-1$	$0$	$0$
tbl_roche_subgroups	👶		$+0.00$	$+2$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
add_forest	👶		$+0.01$	add_forest_handles_extreme_limits_and_character_NA_p_values_safely
add_forest	👶		$+13.76$	add_forest_table_engine_flextable_works
add_hierarchical_count_row	💔	$1.17$	$+2.68$	add_hierarchical_count_row_works
forestplot	💀	$0.04$	$-0.04$	test_g_forest_works
gg_km	💔	$0.21$	$+1.58$	gg_km_works_with_default_inputs
tbl_baseline_chg	💚	$13.85$	$-12.47$	tbl_baseline_chg_works
tbl_hierarchical_rate_by_grade	💔	$1.09$	$+3.62$	tbl_hierarchical_rate_by_grade_works
tbl_roche_subgroups	👶		$+23.10$	tbl_roche_subgroups_time_to_event_NULL_works
tbl_roche_subgroups	👶		$+0.00$	tbl_roche_subgroups_time_to_event_works
tbl_survfit_quantiles	💚	$5.44$	$-4.98$	tbl_survfit_quantiles_works
theme_gtsummary_roche	💚	$5.17$	$-3.32$	theme_gtsummary_roche_works

Results for commit b21b008

♻️ This comment has been updated with latest results.

[BFalquet]

Nice work but apparently the version of tidyselect was updated and using an external vector in selections was deprecated. => use NSE or all_of (there are couple of occurences). Also we get a warning in the .determine_ggplot_header and ..plot_centered_axis as well as in couple of other unmodified function because we dont use .data. add them to utils::globalVariables or use .data/.env

[Melkiades]

Nice work but apparently the version of tidyselect was updated and using an external vector in selections was deprecated. => use NSE or all_of (there are couple of occurences). Also we get a warning in the .determine_ggplot_header and ..plot_centered_axis as well as in couple of other unmodified function because we dont use .data. add them to utils::globalVariables or use .data/.env

Yes I saw the first issue but if you follow it, it seems to be related to process_selectors which is a cards function... I will investigate the second issue!

[Melkiades]

@BFalquet @shajoezhu I think now this is complete! I added some edge cases ;)

[shajoezhu]

hi @Melkiades , tests still failing. can you take a look please.

[shajoezhu]

hi @walkowif , I was wondering do you know why the CLA is failing? Thanks

[walkowif]

@shajoezhu Even though in the check summary it appears as if CLA was failing, it's not.

The failing check is Unit Tests Summary and CLA is in fact passing - they are only grouped together under pull_request_target CI/CD event.

[github-actions]

Code Coverage Summary

Filename                               Stmts    Miss  Cover    Missing
-----------------------------------  -------  ------  -------  ------------------------------------------------------------------------------------------------
R/add_blank_rows.R                        63       0  100.00%
R/add_difference_row.R                   101       0  100.00%
R/add_forest_utils.R                      97      10  89.69%   76-79, 94-100
R/add_forest.R                           137       0  100.00%
R/add_hierarchical_count_row.R            33       0  100.00%
R/annotate_gg_km.R                       145       9  93.79%   86-89, 108-112
R/crane-package.R                          2       2  0.00%    25-26
R/deprecated.R                             6       6  0.00%    15-21
R/get_cox_pairwise_df.R                   50      13  74.00%   68-71, 74-77, 82, 92-95
R/gg_km_utils.R                          102      16  84.31%   94, 134-151, 167
R/gg_km.R                                143      37  74.13%   54-57, 74, 101, 175-180, 183-186, 196-198, 203-204, 238-240, 247-250, 254, 265-269, 282, 284-286
R/label_roche.R                           72       0  100.00%
R/modify_header_rm_md.R                   18       2  88.89%   35-36
R/modify_zero_recode.R                    13       0  100.00%
R/tbl_baseline_chg.R                     186       0  100.00%
R/tbl_hierarchical_rate_and_count.R      148       0  100.00%
R/tbl_hierarchical_rate_by_grade.R       271       3  98.89%   162-164
R/tbl_listing.R                           35       0  100.00%
R/tbl_null_report.R                        9       0  100.00%
R/tbl_roche_subgroups.R                  128       0  100.00%
R/tbl_roche_summary.R                     64       0  100.00%
R/tbl_shift.R                            116       0  100.00%
R/tbl_survfit_quantiles.R                132       1  99.24%   295
R/tbl_survfit_times.R                     92       0  100.00%
R/theme_gtsummary_roche.R                 78       0  100.00%
R/utils.R                                 36       0  100.00%
TOTAL                                   2277      99  95.65%

Diff against main

Filename                   Stmts    Miss  Cover
-----------------------  -------  ------  --------
R/add_forest_utils.R         +97     +10  +89.69%
R/add_forest.R              +137       0  +100.00%
R/tbl_roche_subgroups.R       +9    -119  +100.00%
TOTAL                       +243    -109  +9.32%

Results for commit: f018e93

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[Melkiades]

Hi @walkowif, I think w/o {broom.helpers} tbl_regression does not work well. Could we add it to macos systems? I will add a skip if not installed meanwhile.

Error in loadNamespace(x): there is no package called 'broom.helpers'

[walkowif]

@Melkiades Most likely this is because broom.helpers was removed from DESCRIPTION in this PR.

It's missing from .github/pkg.lock in this PR:

I compared that with .github/pkg.lock in R CMD check workflow in #166:

[shajoezhu]

let's add it into suggest, i think it will be fine

[shajoezhu]

@Melkiades one last error in the check

[shajoezhu]

hey guys, this looks good to me now. I am going to merge this in and unblock the downstream, we can refactor this if needs.