221 new ard ard for tables 32 and 33 #241

aassuied-ps · 2024-09-04T07:09:26Z

Pull Request

Closes #221

Not fully like table_02

Update to stick with table 05

Definition modified (minimum value instead of maximum)

….com/pharmaverse/cardinal into 221-new-ard-ard-for-tables-32-and-33

github-actions · 2024-09-04T07:34:55Z

Code Coverage Summary

Filename            Stmts    Miss  Cover    Missing
----------------  -------  ------  -------  ---------
R/fda-fig_01.R         75       0  100.00%
R/fda-fig_02.R         75       0  100.00%
R/fda-fig_03.R        107       0  100.00%
R/fda-fig_14.R        115       0  100.00%
R/fda-table_02.R      166       0  100.00%
R/fda-table_03.R       35       0  100.00%
R/fda-table_04.R       63       0  100.00%
R/fda-table_05.R       61       0  100.00%
R/fda-table_06.R       76       0  100.00%
R/fda-table_07.R       35       0  100.00%
R/fda-table_08.R       46       0  100.00%
R/fda-table_09.R      329       0  100.00%
R/fda-table_10.R       26       0  100.00%
R/fda-table_11.R       42       0  100.00%
R/fda-table_12.R       40       0  100.00%
R/fda-table_13.R       20       0  100.00%
R/fda-table_14.R       27       0  100.00%
R/fda-table_15.R       32       0  100.00%
R/fda-table_16.R       32       0  100.00%
R/fda-table_17.R       32       0  100.00%
R/fda-table_18.R       32       0  100.00%
R/fda-table_20.R       71       0  100.00%
R/fda-table_21.R       78       0  100.00%
R/fda-table_22.R       77       0  100.00%
R/fda-table_32.R       83       0  100.00%
R/fda-table_33.R       88       0  100.00%
R/fda-table_34.R       41       0  100.00%
R/fda-table_35.R       23       0  100.00%
R/fda-table_36.R       30       0  100.00%
R/fda-table_38.R       39       0  100.00%
R/utils.R              28       0  100.00%
TOTAL                2024       0  100.00%

Diff against main

Filename            Stmts    Miss  Cover
----------------  -------  ------  --------
R/fda-table_32.R      -11       0  +100.00%
R/fda-table_33.R       -7       0  +100.00%
TOTAL                 -18       0  +100.00%

Results for commit: 96524b2

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2024-09-04T07:35:59Z

Unit Tests Summary

1 files 30 suites 1m 14s ⏱️
130 tests 130 ✅ 0 💤 0 ❌
484 runs 358 ✅ 126 💤 0 ❌

Results for commit 96524b2.

♻️ This comment has been updated with latest results.

github-actions · 2024-09-04T07:36:03Z

Unit Test Performance Difference

Additional test case details

Test Suite	$Status$	Time on `main`	$±Time$	Test Case
fda-table_32	👶		$+1.05$	Table_32_generation_missing_values_and_ADSL
fda-table_32	💔	$0.24$	$+1.45$	Table_32_generation_works_with_custom_values
fda-table_32	💔	$0.25$	$+1.05$	Table_32_generation_works_with_default_values
fda-table_32	💀	$1.46$	$-1.46$	Table_32_gtsum_generation_missing_values_and_ADSL
fda-table_32	💀	$1.45$	$-1.45$	Table_32_gtsum_generation_works_with_custom_values
fda-table_32	💀	$1.03$	$-1.03$	Table_32_gtsum_generation_works_with_default_values
fda-table_33	👶		$+1.04$	Table_33_generation_missing_values_and_ADSL
fda-table_33	💔	$0.38$	$+1.35$	Table_33_generation_works_with_custom_values
fda-table_33	💀	$1.29$	$-1.29$	Table_33_gtsum_generation_missing_values_and_ADSL
fda-table_33	💀	$1.28$	$-1.28$	Table_33_gtsum_generation_works_with_custom_values
fda-table_33	💀	$0.98$	$-0.98$	Table_33_gtsum_generation_works_with_default_values

Results for commit 98e901e

♻️ This comment has been updated with latest results.

Needed for filtering in tables 32/33 and probably others

Table 33 left to be done

….com/pharmaverse/cardinal into 221-new-ard-ard-for-tables-32-and-33

Only table 32 has been updated for review purpose. If changes are approved, the same will be done for table 33.

….com/pharmaverse/cardinal into 221-new-ard-ard-for-tables-32-and-33

Programs only. unit tests will follow so as website.

aassuied-ps · 2024-11-19T11:23:30Z

The error in tests is the following:

Error: `everything()` must be used within a *selecting* function.

It comes from gtsummary::modify_footnote():

# Example 2 ----------------------------------
# updating headers, remove all footnotes, add spanning header
tbl |>
  modify_header(all_stat_cols() ~ "**{level}**, N = {n} ({style_percent(p)}%)") |>
  modify_footnote(everything() ~ NA) |>
  modify_spanning_header(all_stat_cols() ~ "**Treatment Received**")

The function is working well though. I don't know what to do to avoid this specific message with testthat.

edelarua · 2024-11-19T20:21:07Z

The error in tests is the following:
Error: `everything()` must be used within a *selecting* function.
The function is working well though. I don't know what to do to avoid this specific message with testthat.

Hi @aassuied-ps,

I think we should leave the extra formatting as default as we can, i.e. just leave the footnotes as is. The good thing about using gtsummary is that it's easy for users to modify tables in post-processing, so they can choose to replace the default footnotes if needed.

aassuied-ps · 2024-11-21T10:11:50Z

Hi @edelarua, thank you very much. It seems good now!

aassuied-ps added 15 commits June 18, 2024 10:40

push draft

86392b2

New try

e2b6404

Create alex_try_like_table_02.R

58b1fc4

Not fully like table_02

push

ff36633

updates

e20617f

Update fda-table_32.R

d222eed

Update fda-table_32.R

05c35cb

Update fda-table_32.R

4412a54

Update fda-table_32.R

70968a6

Update to stick with table 05

Update fda-table_32.R

e1f8fa9

push testthat

ba2190c

update quarto for table 32

0400b0e

update quarto

6d4dced

Update table 33

68759c7

Definition modified (minimum value instead of maximum)

add subset argument

3bf694e

aassuied-ps linked an issue Sep 4, 2024 that may be closed by this pull request

[New ARD] ARD for tables 32 and 33 #221

Open

aassuied-ps added the ARD label Sep 4, 2024

aassuied-ps and others added 5 commits September 4, 2024 09:20

Merge branch 'main' into 221-new-ard-ard-for-tables-32-and-33

84b7a53

[skip style] [skip vbump] Restyle files

ab459d8

[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

17a8880

Update for code coverage

f258fc9

Merge branch '221-new-ard-ard-for-tables-32-and-33' of https://github…

576d71e

….com/pharmaverse/cardinal into 221-new-ard-ard-for-tables-32-and-33

aassuied-ps and others added 5 commits September 4, 2024 09:51

add admiraldev::assert_filter_cond

8385d74

Needed for filtering in tables 32/33 and probably others

push

100cc64

Merge branch 'main' into 221-new-ard-ard-for-tables-32-and-33

398a332

update table 32

ff86d99

Table 33 left to be done

[skip style] [skip vbump] Restyle files

278262a

aassuied-ps and others added 22 commits October 10, 2024 18:31

push

864e323

[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

178afc8

up

a712ff9

Merge branch '221-new-ard-ard-for-tables-32-and-33' of https://github…

cad0b14

….com/pharmaverse/cardinal into 221-new-ard-ard-for-tables-32-and-33

up

cdcf404

Simplify and reconfigure make_table_32

1a9fd6b

Update docs

76c414f

Fix template

bebc238

push PR

0507a9c

Only table 32 has been updated for review purpose. If changes are approved, the same will be done for table 33.

[skip style] [skip vbump] Restyle files

82cbc4e

push

d911878

[skip style] [skip vbump] Restyle files

0c977f4

[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

115fb75

update

bb93beb

Merge branch '221-new-ard-ard-for-tables-32-and-33' of https://github…

27331a8

….com/pharmaverse/cardinal into 221-new-ard-ard-for-tables-32-and-33

[skip style] [skip vbump] Restyle files

f004ff4

push

af20e37

Programs only. unit tests will follow so as website.

[skip style] [skip vbump] Restyle files

ef36bf0

[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

9949908

tests

a4a767a

push quarto

6a626ee

push

b554cfd

push

a7e7e86

aassuied-ps added 4 commits November 21, 2024 09:48

delete modify_footnote

f08f6e3

update man and cardinal.R

7521d0b

Add tests

68ac736

nocov handling

96524b2

Provide feedback

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221 new ard ard for tables 32 and 33 #241

221 new ard ard for tables 32 and 33 #241

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edelarua commented Nov 19, 2024

aassuied-ps commented Nov 21, 2024

221 new ard ard for tables 32 and 33 #241

Are you sure you want to change the base?

221 new ard ard for tables 32 and 33 #241

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aassuied-ps commented Sep 4, 2024

Pull Request

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Code Coverage Summary

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Unit Tests Summary

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Unit Test Performance Difference

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