Fix kmplot par error and more

gravesti commented 3 months ago

fixes error reported in #122 by only restoring changed pars
adds more tests for plots
improve time scale functions:
- set the default time scale
- add tests
improve basic_kmplot
- allow time_grid = NULL and derive using pretty()
- allow time_scale = NULL to use the default, normally would do no transformation
- return invisible(NULL)

github-actions[bot] commented 3 months ago

Code Coverage Summary

Filename               Stmts    Miss  Cover    Missing
-------------------  -------  ------  -------  -------------------------------------------------------------------------------------------------------------------
R/binary-helper.R         59       7  88.14%   14, 18, 21, 24, 28, 31, 36
R/bootstrap.R             23      23  0.00%    54-88
R/bucher.R                62       5  91.94%   103, 107, 111, 186-187
R/data_generation.R       20      20  0.00%    36-73
R/maic_anchored.R        348      46  86.78%   89-96, 101-104, 108, 111, 115, 118-121, 124-127, 132, 137, 140, 158-163, 214, 275, 281, 426-435, 444, 450, 521, 538
R/maic_unanchored.R      253      33  86.96%   80-87, 90-91, 96, 99-102, 105-108, 113, 122, 125, 148-155, 184, 241, 248, 357, 364
R/matching.R             244     145  40.57%   65, 70-72, 77-80, 87-94, 139, 175, 214, 256-515
R/plot_km.R              447      46  89.71%   53, 56, 59, 73-103, 294, 297-299, 314-317, 349, 405, 481, 484, 487, 499-500
R/plot_km2.R             107      22  79.44%   50, 59, 62, 65, 87-93, 120-128, 131, 175
R/process_data.R         101      44  56.44%   49-51, 56, 71-74, 80, 92-93, 183, 216-280
R/reporting.R             59       0  100.00%
R/survival-helper.R       30       1  96.67%   63
R/time-helper.R           20       3  85.00%   32, 58-59
R/utils.R                 12      10  16.67%   4, 11-20
R/zzz.R                    1       1  0.00%    2
TOTAL                   1786     406  77.27%

Diff against main

Filename               Stmts    Miss  Cover
-------------------  -------  ------  -------
R/matching.R              -1      -1  +0.17%
R/plot_km.R               -2    -327  +72.78%
R/survival-helper.R        0      -2  +6.67%
R/time-helper.R          +11      -1  +29.44%
TOTAL                     +8    -331  +18.72%

Results for commit: d35803d6e5fa538d349212d535faf12b48dbef12

Minimum allowed coverage is 80%

:recycle: This comment has been updated with latest results

github-actions[bot] commented 3 months ago

Unit Tests Summary

1 files 9 suites 7s :stopwatch: 29 tests 28 :white_check_mark: 1 :zzz: 0 :x: 96 runs 88 :white_check_mark: 8 :zzz: 0 :x:

Results for commit d35803d6.

github-actions[bot] commented 3 months ago

Unit Test Performance Difference

Test Suite	$Status$	Time on `main`	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
plot_km2	👶		$+1.80$	$+1$	$+1$	$0$	$0$
time-helper	👶		$+0.03$	$+10$	$0$	$0$	$0$

Additional test case details

| Test Suite | $Status$ | Time on `main` | $±Time$ | Test Case | |:-----|:----:|:----:|:----:|:-----| | plot_km2 | 👶 | | $+1.80$ | kmplot2_works | | plot_km | 💀 | $1.74$ | $-1.74$ | kmplot2_works | | plot_km | 👶 | | $+0.12$ | kmplot_works_all | | plot_km | 👶 | | $+0.12$ | kmplot_works_by_arm | | plot_km | 👶 | | $+0.13$ | kmplot_works_by_trial | | plot_km | 👶 | | $+0.48$ | ph_diagplot_works_for_anchored_data | | plot_km | 👶 | | $+0.25$ | ph_diagplot_works_for_unanchored_data | | time-helper | 👶 | | $+0.03$ | setting_time_factors_works |

Results for commit dc040b3bf082cc33a176e789c8339e21c0ec42f2

♻️ This comment has been updated with latest results.

hta-pharma / maicplus