[Melkiades]

What changes are proposed in this pull request?

• gg_pkc_lineplot() now adds a single x scale instead of two, so it no longer reports "Scale for x is already present" on every call with a numeric time_var. The expand setting that the discarded scale carried is now applied. (gg_pkc_lineplot() adds two x scales and hardcodes the error bar cap width #322)
• gg_pkc_lineplot() gains an x_breaks argument to set the breaks of a numeric x-axis, for time ranges too wide to label every timepoint. The default NULL keeps a break on every observed timepoint. (gg_pkc_lineplot() adds two x scales and hardcodes the error bar cap width #322)
• gg_pkc_lineplot() and gg_lineplot() gain an errorbar_width argument to set the width of the error bar caps, previously fixed at 0.45. (gg_pkc_lineplot() adds two x scales and hardcodes the error bar cap width #322)

All three are backwards compatible: every default reproduces the current output.

Detail

The x scale bug was visible in our own test suite. Before this change, Scale for x is already present. Adding another scale for x, which will replace the existing scale. appeared on essentially every gg_pkc_lineplot() test; after it, the full suite reports it zero times. Because ggplot2 kept the second scale, the expand = expansion(mult = 0.05) on the first one had never had any effect.

The two new arguments come from template work on PKCG03, where the lack of them was the stated reason for dropping gg_pkc_lineplot() and hand-writing the plot in raw ggplot2. That trade loses the input validation, the invalid stat/variability guard, the factor/numeric time_var handling and the LLOQ line. Both gaps are small enough to close directly.

x_breaks accepts a vector or a break function, so a 0 to 600 hour profile can use seq(0, 600, by = 100) or scales::breaks_pretty() instead of a tick per timepoint.

The three man/*.Rd files were updated by hand: the local roxygen2 is 7.3.3 while DESCRIPTION pins 8.1.0, and running the older version rewrote unrelated files. If CI regenerates docs with 8.1.0 and shows a diff in those three files, that diff is formatting only.

Reference GitHub issue associated with pull request. closes #322

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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

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Unit Tests Summary

  1 files  338 suites   1m 50s ⏱️
338 tests 338 ✅ 0 💤 0 ❌
987 runs  987 ✅ 0 💤 0 ❌

Results for commit 2067888.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
gg_pkc_boxplot	👶		$+0.00$	$+2$	$0$	$0$	$0$
modify_header_rm_md	💔	$0.10$	$+1.10$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
add_forest	💚	$4.55$	$-1.15$	add_forest_table_engine_flextable_works
add_grade_column	💚	$7.95$	$-1.09$	add_grade_column_works_on_a_standalone_tbl_hierarchical_rate_by_grade
annotate_gg	💚	$3.61$	$-3.22$	annotate_lineplot_df_warns_if_plot_is_not_generated_by_gg_lineplot
annotate_gg_km	💔	$0.01$	$+3.17$	annotate_riskdf_handles_all_branches_and_inputs
gg_lineplot	👶		$+0.00$	gg_lineplot_errorbar_width_sets_the_error_bar_cap_width
gg_lineplot	💚	$1.26$	$-1.10$	gg_lineplot_input_validation_catches_invalid_statistical_combinations
gg_pkc_boxplot	👶		$+1.68$	gg_pkc_boxplot_catches_invalid_arguments_and_missing_inputs
gg_pkc_boxplot	👶		$+0.01$	gg_pkc_boxplot_computes_tukey_whiskers_and_flags_outliers
gg_pkc_boxplot	👶		$+0.00$	gg_pkc_boxplot_converts_time_var_to_a_discrete_factor_regardless_of_input_type
gg_pkc_boxplot	👶		$+0.00$	gg_pkc_boxplot_dodges_boxes_whiskers_outliers_and_the_mean_marker_together
gg_pkc_boxplot	👶		$+0.02$	gg_pkc_boxplot_drops_non_positive_values_before_log_transforming
gg_pkc_boxplot	👶		$+0.00$	gg_pkc_boxplot_passes_quantile_type_through_to_stats_quantile
gg_pkc_boxplot	👶		$+0.01$	gg_pkc_boxplot_percentile_and_minmax_whiskers_do_not_flag_the_same_outlier
gg_pkc_boxplot	👶		$+0.00$	gg_pkc_boxplot_toggles_the_mean_marker_layer_with_show_mean
gg_pkc_lineplot	👶		$+0.00$	gg_pkc_lineplot_adds_a_single_x_scale_and_honours_x_breaks
gg_pkc_lineplot	👶		$+0.00$	gg_pkc_lineplot_dodges_error_bars_to_match_the_line_point_layers
gg_pkc_lineplot	👶		$+0.00$	gg_pkc_lineplot_passes_errorbar_width_to_the_error_bar_caps
gg_utils	💚	$1.23$	$-1.09$	df2gg_aligned_input_validation_and_error_handling_works
modify_header_rm_md	💔	$0.10$	$+1.10$	strip_md_bold_works_with_gtsummary_table
tbl_baseline_chg	💚	$13.37$	$-2.60$	tbl_baseline_chg_works
tbl_hierarchical_rate_and_count	💚	$10.45$	$-1.65$	tbl_hierarchical_rate_and_count_works
tbl_hierarchical_rate_by_grade	💚	$12.87$	$-3.78$	tbl_hierarchical_rate_by_grade_works
tbl_mmrm	💔	$0.41$	$+1.85$	se_calculates_standard_error_correctly
tbl_proportion	💚	$5.70$	$-2.94$	tbl_proportion_binary_summary_works
tbl_rmpt	💔	$3.36$	$+1.64$	tbl_rmpt_works_with_default_parameters_Example_1_
tbl_roche_subgroups	💚	$10.08$	$-3.45$	tbl_roche_subgroups_time_to_event_NULL_works
tbl_shift	💔	$0.15$	$+1.73$	tbl_shift_strata_location_
tbl_survfit_times	💚	$2.28$	$-2.09$	tbl_survfit_times_works

Results for commit a9eacd7

♻️ 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/add_label_column.R                        26       0  100.00%
R/add_proportion_difference.R              150       1  99.33%   245
R/add_proportion_odds_ratio.R               57       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                             94       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                            113       0  100.00%
R/gg_mmrm_lineplot.R                       102       1  99.02%   106
R/gg_pkc_boxplot.R                         195       5  97.44%   108, 136-139
R/gg_pkc_lineplot.R                        118       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                    37       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                             36       0  100.00%
R/tbl_mmrm.R                               344       6  98.26%   452-456, 548
R/tbl_null_report.R                         10       0  100.00%
R/tbl_proportion.R                         141      13  90.78%   100-103, 107-111, 114-117
R/tbl_rmpt.R                               157      12  92.36%   299-304, 316-321
R/tbl_roche_subgroups.R                    157       0  100.00%
R/tbl_roche_summary.R                       64       0  100.00%
R/tbl_shift.R                              111       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                                     5632     149  97.35%

Diff against main

Filename               Stmts    Miss  Cover
-------------------  -------  ------  --------
R/gg_lineplot.R           -8       0  +100.00%
R/gg_pkc_boxplot.R      +195      +5  +97.44%
R/gg_pkc_lineplot.R      +20       0  +100.00%
TOTAL                   +207      +5  +0.01%

Results for commit: 2067888

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[qiliu1013]

Hi @Melkiades,

• gg_pkc_lineplot() dodges its line/point layers but not the error bars, so 'groups' error bars would otherwise overlap instead of sitting side by side (see gg_pkc_lineplot() adds two x scales and hardcodes the error bar cap width #322) - patch the error bar layer to match. Could you please add the dodge functions on the error bars?

errorbar_idx <- which(vapply(plt_pkcg03$layers, function(l) inherits(l$geom, "GeomErrorbar"), logical(1))) plt_pkcg03$layers[[errorbar_idx]]$position <- ggplot2::position_dodge(width = 0.2)

• Additionally, I got following message, which is a bit confused, we want the time_var to be numeric and we won't show the summary table under the table. Can you please remove this message from the function?

"We encourage to supply time_var as a factor, since it supports correct decimals formatting in the summary table."

• The y scale will be reassigned when apply log scale based on the actual range of log y, could you please remove the message below.

Scale for y is already present. Adding another scale for y, which will replace the existing scale.

Thanks,
Qi

[github-actions]

✅ All contributors have signed the CLA
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[wzfrank]

I have read the CLA Document and I hereby sign the CLA

[Melkiades]

It looks super good to me!! Thanks Zhen

[wzfrank]

All functions are good and well tested.