79 add binary endpoints to wrapper anchored function #112

hoppanda · 2024-06-28T07:14:24Z

No description provided.

…table 67 add function to expand 2x2 table

…g report_table function

…ile CI option and cli progress bar

…nto update-with-bootstrap-code

Update with bootstrap code

…nto update-to-main

Update to main

R/maic_anchored.R

inst/examples/maic_anchored_ex.R

inst/examples/maic_unanchored_binary_ex.R

inst/examples/maic_unanchored_ex.R

tests/testthat.R

gravesti · 2024-07-02T09:54:53Z

@hoppanda Still need some tests for anchored binary

…f github.com:hta-pharma/maicplus into 79-add-binary-endpoints-to-wrapper-anchored-function

github-actions · 2024-07-12T12:30:19Z

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             245     146  40.41%   65, 70-72, 77-80, 87-94, 139, 175, 214, 256-516
R/plot_km.R              449     373  16.93%   46-598
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       3  90.00%   63, 66-67
R/time-helper.R            9       4  55.56%   22, 37-38, 52
R/utils.R                 12      10  16.67%   4, 11-20
R/zzz.R                    1       1  0.00%    2
TOTAL                   1778     737  58.55%

Diff against main

Filename             Stmts    Miss  Cover
-----------------  -------  ------  -------
R/bucher.R              +7      +2  -2.61%
R/maic_anchored.R     +171     +12  +5.99%
R/reporting.R            0      -1  +1.69%
TOTAL                 +178     +13  +3.80%

Results for commit: d398b9b

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

…function

gravesti · 2024-07-12T14:39:24Z

R/maic_anchored.R

+  tags <- paste0(c("IPD/", "weighted IPD/", "AgD/"), endpoint_name)
+  res$inferential[["report_overall_robustCI"]] <- rbind(
+    report_table_binary(binobj_ipd, tag = tags[1], eff_measure = eff_measure),
+    report_table_binary(binobj_ipd_adj, res_AB, tag = tags[2], eff_measure = eff_measure),


@hoppanda Trying to follow what's being reported here. I think res_AB should actually be the results for the weighted AC comparison, right? The A v B should only appear in the last line?
eg
A v C
A v C weighted
B v C
A v B

Suggested change

report_table_binary(binobj_ipd_adj, res_AB, tag = tags[2], eff_measure = eff_measure),

report_table_binary(binobj_ipd_adj, res_AB, tag = tags[2], eff_measure = eff_measure),

I've updated this. Can you check @hoppanda ?

github-actions · 2024-07-18T11:27:28Z

Unit Tests Summary

1 files 7 suites 6s ⏱️
23 tests 22 ✅ 1 💤 0 ❌
76 runs 73 ✅ 3 💤 0 ❌

Results for commit d398b9b.

♻️ This comment has been updated with latest results.

github-actions · 2024-07-18T11:27:31Z

Unit Test Performance Difference

Additional test case details

Test Suite	$Status$	Time on `main`	$±Time$	Test Case
maic_anchored	👶		$+0.41$	maic_anchored_for_binary_case_gives_the_expected_result

Results for commit 1765402

♻️ This comment has been updated with latest results.

…function

gravesti

@hoppanda @MikeJSeo Let's quickly discuss this tomorrow then merge if possible

hoppanda and others added 27 commits March 15, 2024 08:02

add binary-helper.R

01cbf8b

tempo update

f42919c

update

b57bcd3

reformat as anchored wrapper function and add in binary initial script

6c01591

separate binary inferential part to a separate function

e0bcd19

refine binary inferential function

4053945

Merge pull request #91 from hta-pharma/67-add-function-to-expand-2x2-…

dc73d8f

…table 67 add function to expand 2x2 table

workable binary unanchor

d2ce708

add unanchored binary example

818cc53

keep consistency of treatment column name between binary and tte usin…

0135d0f

…g report_table function

make binary bootstrap work with cli progress bar

cd699ff

styler

467327c

update unanchor binary example annotation

45cbd9a

add test for binary helper function

211f6d9

add test for binary unanchored MAIC wrapper

931d83e

add boot quantile function, and test for tte unanchor maic wrapper

433ebb8

update document

095f857

deactive unnecessary line in testthat

04bd382

update anchored tte given new report function and add bootstrap quant…

9e3b34d

…ile CI option and cli progress bar

add binary

24cf75d

update

cb6958c

update print of maicplus bucher object and add reformat object

51ca57b

Merge branch '79-add-binary-endpoints-to-wrapper-anchored-function' i…

e425511

…nto update-with-bootstrap-code

Merge pull request #107 from hta-pharma/update-with-bootstrap-code

bf5b761

Update with bootstrap code

Merge branch '79-add-binary-endpoints-to-wrapper-anchored-function' i…

9ca4431

…nto update-to-main

Merge pull request #110 from hta-pharma/update-to-main

5e1d770

Update to main

update

1bf9b9b

hoppanda linked an issue Jun 28, 2024 that may be closed by this pull request

add binary endpoints to wrapper anchored function #79

Closed

github-actions bot and others added 2 commits June 28, 2024 07:16

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gravesti self-assigned this Jun 28, 2024