Add pk helper functions

[qiliu1013]

What changes are proposed in this pull request?

• Style this entry in a way that can be copied directly into NEWS.md. (#, @)

Provide more detail here as needed.

Add cv(), geom_cv(), geom_mean(), fmt_3sig() and impuation_rules for the PK TLGs.

Close #287

---

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

• If a bug was fixed, a unit test was added.
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• 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).
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[github-actions]

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[qiliu1013]

Hi @shajoezhu @wzfrank,

Could you please help with the tests on the functions? Is there a certain format I need to follow? So some simple tests below are fine.

`
test_that("cv() works", {
expect_equal(cv(c(1, 2, 3, 4, 5)), 52.70463, tolerance = 1e-4)
expect_true(is.na(cv(c(NA, NA))))
})

test_that("geom_mean() returns NA for non-positive values", {
expect_equal(geom_mean(c(1, 2, 4)), exp(mean(log(c(1, 2, 4)))))
expect_true(is.na(geom_mean(c(1, -1, 3))))
})

test_that("fmt_3sig() formats correctly", {
expect_equal(fmt_3sig(0.001234), "0.00123")
expect_equal(fmt_3sig(NA), NA_character_)
})
`

[github-actions]

Unit Tests Summary

  1 files  260 suites   2m 15s ⏱️
260 tests 260 ✅ 0 💤 0 ❌
760 runs  760 ✅ 0 💤 0 ❌

Results for commit 8dbb153.

♻️ 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	💚	$5.96$	$-1.42$	add_blank_rows_works
add_grade_column	💚	$18.40$	$-4.76$	add_grade_column_works_on_a_standalone_tbl_hierarchical_rate_by_grade
annotate_gg_pkc	💚	$2.76$	$-2.66$	annotate_pkc_df_warns_when_given_a_standard_ggplot_object
gg_km	💔	$0.25$	$+1.99$	gg_km_works_and_handles_annotations_correctly
tbl_baseline_chg	💚	$18.64$	$-4.96$	tbl_baseline_chg_works
tbl_hierarchical_incidence_rate	💚	$15.04$	$-1.96$	tbl_hierarchical_incidence_rate_runs_with_minimum_arguments
tbl_hierarchical_rate_and_count	💚	$22.29$	$-5.71$	tbl_hierarchical_rate_and_count_works
tbl_hierarchical_rate_by_grade	💚	$18.37$	$-7.66$	tbl_hierarchical_rate_by_grade_works
tbl_mmrm	💚	$5.89$	$-1.49$	se_calculates_standard_error_correctly
tbl_rmpt	💚	$12.54$	$-3.10$	tbl_rmpt_works_with_default_parameters_Example_1_
tbl_roche_subgroups	💚	$3.31$	$-1.80$	tbl_roche_subgroups_time_to_event_NULL_works
tbl_roche_summary	💔	$2.56$	$+1.54$	tbl_roche_summary_works
tbl_survfit_quantiles	💚	$5.77$	$-1.51$	tbl_survfit_quantiles_works
tbl_with_pools	💚	$9.73$	$-2.78$	tbl_with_pools_validates_inputs_correctly
theme_gtsummary_roche	💚	$6.34$	$-1.67$	theme_gtsummary_roche_works

Results for commit 408ec74

♻️ 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                         92       0  100.00%
R/annotate_gg.R                             81       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_zero_recode.R                      20       1  95.00%   64
R/pk_helper.R                               30      30  0.00%    14-125
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                          9       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                          64       0  100.00%
R/theme_gtsummary_roche.R                   87       1  98.85%   61
R/utils.R                                   42       0  100.00%
TOTAL                                     4393     154  96.49%

Diff against main

Filename         Stmts    Miss  Cover
-------------  -------  ------  --------
R/pk_helper.R      +30     +30  +100.00%
TOTAL              +30     +30  -0.66%

Results for commit: 8dbb153

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results