Lineplot@main

[BFalquet]

This pull request introduces a new feature for generating line plots with summary statistics tables, along with supporting helper functions and documentation. The main additions are the g_lineplot(), g_lineplot_table(), and preprocess_lineplot_data() functions, which streamline the process of visualizing and summarizing numeric data in clinical trial datasets. The changes also include updates to documentation, package dependencies, and exports to ensure these new features are accessible and well-documented.

New Line Plot Functionality:

• Added g_lineplot() for creating line plots from pre-calculated statistics, supporting stratification, error bars, and customization of colors and line types.
• Added g_lineplot_table() for generating a ggplot-formatted table to display summary statistics beneath the main plot.
• Added preprocess_lineplot_data() to clean, expand, join, and compute summary statistics from raw data, preparing it for plotting.

Helper Functions and Documentation:

• Added calc_stats() for calculating N, mean, standard deviation, and confidence intervals for a numeric vector, with full documentation and examples. [1] [2]
• Added detailed documentation for all new functions and updated the package website reference section to include them. [1] [2] [3] [4]

Package Infrastructure Updates:

• Exported new functions and updated imports in NAMESPACE and DESCRIPTION, including dependency version bump for scales. [1] [2] [3] [4] [5]
• Expanded inst/WORDLIST to include relevant terminology for clinical trial and plotting contexts. [1] [2]

[github-actions]

✅ All contributors have signed the CLA
_{Posted by the CLA Assistant Lite bot.}

[github-actions]

Unit Tests Summary

  1 files   81 suites   1m 53s ⏱️
 81 tests  81 ✅ 0 💤 0 ❌
228 runs  228 ✅ 0 💤 0 ❌

Results for commit f144ce7.

♻️ 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_lineplot	👶		$+0.01$	$+13$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
gg_lineplot	👶		$+0.39$	calc_stats_works_correctly
gg_lineplot	👶		$+0.00$	g_lineplot_table_works_correctly
gg_lineplot	👶		$+0.01$	g_lineplot_works_correctly
gg_lineplot	👶		$+0.01$	preprocess_lineplot_data_works_correctly
tbl_hierarchical_rate_by_grade	💔	$2.06$	$+1.26$	tbl_hierarchical_rate_by_grade_works
tbl_survfit_quantiles	💚	$3.18$	$-1.23$	tbl_survfit_quantiles_works
tbl_survfit_times	💔	$0.26$	$+1.23$	tbl_survfit_times_works
theme_gtsummary_roche	💚	$4.51$	$-1.19$	theme_gtsummary_roche_works

Results for commit f957636

♻️ 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                           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%    26-27
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/gg_lineplot.R                           99       2  97.98%   145, 148
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                                   2376     101  95.75%

Diff against main

Filename           Stmts    Miss  Cover
---------------  -------  ------  -------
R/gg_lineplot.R      +99      +2  +97.98%
TOTAL                +99      +2  +0.10%

Results for commit: f144ce7

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[BFalquet]

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

[shajoezhu]

approve to unblock merging