Add modular pipeline vignette

[Melkiades]

What changes are proposed in this pull request?

• Add vignette documenting the compute → tabulate → customize pipeline pattern. (Add vignette: modular TLG pipeline (compute → tabulate → customize) #249)

Reference GitHub issue associated with pull request.
closes #249

---

Covers:

• The three layers using tbl_coxph() as primary example
• Where digits/formatting are set at each layer and how to change them
• Other modular components: add_grade_column(), add_forest(), tbl_with_pools()
• How to swap layers (bring your own data frame, custom .tbl_fun, gtsummary post-processing)

Pre-review checklist

• PR branch is up to date with main
• Documentation is complete
• Tests pass locally
• NEWS entry (not needed — vignette only)

[Melkiades]

@mhallal1 this is a bit of an idea on how to make code more intuitive and explicit (also against the overly wrapping tern counterpart). I think we can merge it as is and follow-up if ever it gets any attention. Our user documentation must be in tlg-catalog mainly. This vignette is a bit more for {crane} devs or {crane} enthusiasts

[github-actions]

Unit Tests Summary

  1 files  299 suites   1m 41s ⏱️
299 tests 298 ✅ 0 💤 1 ❌
869 runs  868 ✅ 0 💤 1 ❌

For more details on these failures, see this check.

Results for commit 2ada3df.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
add_blank_rows	💚	$5.89$	$-1.76$	add_blank_rows_works
add_forest	💔	$1.68$	$+3.74$	add_forest_table_engine_flextable_works
add_grade_column	💚	$16.17$	$-9.83$	add_grade_column_works_on_a_standalone_tbl_hierarchical_rate_by_grade
add_hierarchical_count_row	💚	$3.05$	$-1.27$	add_hierarchical_count_row_works
annotate_gg	💚	$7.89$	$-5.80$	annotate_lineplot_df_warns_if_plot_is_not_generated_by_gg_lineplot
annotate_gg_km	💚	$3.50$	$-2.54$	annotate_riskdf_handles_all_branches_and_inputs
gg_km	💔	$0.63$	$+2.19$	gg_km_works_and_handles_annotations_correctly
gg_utils	💚	$1.58$	$-1.57$	df2gg_aligned_input_validation_and_error_handling_works
tbl_baseline_chg	💚	$18.70$	$-7.84$	tbl_baseline_chg_works
tbl_coxph	💚	$3.25$	$-1.50$	tbl_coxph_errors_on_invalid_inputs
tbl_hierarchical_incidence_rate	💚	$18.44$	$-9.76$	tbl_hierarchical_incidence_rate_runs_with_minimum_arguments
tbl_hierarchical_rate_and_count	💚	$20.89$	$-12.23$	tbl_hierarchical_rate_and_count_works
tbl_mmrm	💚	$6.45$	$-2.71$	se_calculates_standard_error_correctly
tbl_rmpt	💚	$13.15$	$-11.09$	tbl_rmpt_works_with_default_parameters_Example_1_
tbl_roche_subgroups	💚	$11.86$	$-4.57$	tbl_roche_subgroups_time_to_event_NULL_works
tbl_roche_summary	💚	$5.83$	$-1.89$	tbl_roche_summary_works
tbl_shift	💚	$5.26$	$-3.87$	tbl_shift_strata_location_
tbl_with_pools	💚	$12.11$	$-5.98$	tbl_with_pools_validates_inputs_correctly
theme_gtsummary_roche	💚	$6.52$	$-2.30$	theme_gtsummary_roche_works

Results for commit 9c73400

♻️ This comment has been updated with latest results.

[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                             139       0  100.00%
R/add_hierarchical_count_row.R              33       0  100.00%
R/adjust_stat_columns_wrap.R                29       1  96.55%   59
R/annotate_gg_km.R                         141       0  100.00%
R/annotate_gg_pkc.R                        100       0  100.00%
R/annotate_gg.R                             83       0  100.00%
R/ard_tabulate_abnormal_by_baseline.R       65       0  100.00%
R/crane-package.R                            2       2  0.00%    26-27
R/deprecated.R                              21      21  0.00%    18-54
R/df_add_poolings.R                         41       0  100.00%
R/get_cox_pairwise_df.R                    163       0  100.00%
R/gg_km_utils.R                             39      14  64.10%   20-37
R/gg_km.R                                  143      37  74.13%   55-58, 75, 102, 176-181, 184-187, 197-199, 204-205, 239-241, 248-251, 255, 266-270, 283, 285-287
R/gg_lineplot.R                             94       0  100.00%
R/gg_mmrm_lineplot.R                       102       1  99.02%   106
R/gg_pkc_lineplot.R                         98       0  100.00%
R/gg_utils.R                               222       0  100.00%
R/label_roche.R                             72       0  100.00%
R/modify_header_rm_md.R                     18       2  88.89%   35-36
R/modify_split_caption.R                    26       0  100.00%
R/modify_zero_recode.R                      20       1  95.00%   64
R/pk_helper.R                              499       0  100.00%
R/reverse_difference_ci.R                   33       0  100.00%
R/tbl_baseline_chg.R                       188       0  100.00%
R/tbl_coxph.R                               90       1  98.89%   229
R/tbl_hierarchical_incidence_rate.R        291       4  98.63%   430-433
R/tbl_hierarchical_rate_and_count.R        339      13  96.17%   343, 425, 446-456
R/tbl_hierarchical_rate_by_grade.R         317       3  99.05%   169-171
R/tbl_listing.R                             35       0  100.00%
R/tbl_mmrm.R                               254       1  99.61%   393
R/tbl_null_report.R                         10       0  100.00%
R/tbl_rmpt.R                               157      12  92.36%   299-304, 316-321
R/tbl_roche_subgroups.R                    155       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                  154       0  100.00%
R/tbl_survfit_times.R                       92       0  100.00%
R/tbl_with_pools.R                          79       1  98.73%   317
R/theme_gtsummary_roche.R                   87       1  98.85%   61
R/utils.R                                   42       0  100.00%
TOTAL                                     4914     125  97.46%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  --------
TOTAL             0       0  +100.00%

Results for commit: c365a4f

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results