Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

196-new-table-38 #204

Merged
merged 8 commits into from
Feb 23, 2024
Merged

196-new-table-38 #204

merged 8 commits into from
Feb 23, 2024

Conversation

YoshitoKoujin
Copy link
Collaborator

Pull Request

Closes #196

@YoshitoKoujin YoshitoKoujin linked an issue Jan 26, 2024 that may be closed by this pull request
8 tasks
@YoshitoKoujin YoshitoKoujin changed the title 1st commitment for all documents 196-new-table-38 Jan 26, 2024
Copy link
Contributor

badge

Code Coverage Summary

Filename            Stmts    Miss  Cover    Missing
----------------  -------  ------  -------  ---------
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      214       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_32.R       75       0  100.00%
R/fda-table_33.R       30       0  100.00%
R/fda-table_34.R       30       0  100.00%
R/fda-table_35.R       23       1  95.65%   58
R/fda-table_38.R       37       0  100.00%
R/utils.R              28       0  100.00%
TOTAL                1351       1  99.93%

Diff against main

Filename            Stmts    Miss  Cover
----------------  -------  ------  --------
R/fda-table_38.R      +37       0  +100.00%
TOTAL                 +37       0  -0.01%

Results for commit: f084081

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

Copy link
Contributor

github-actions bot commented Jan 26, 2024

Unit Test Performance Difference

Test Suite $Status$ Time on main $±Time$ $±Tests$ $±Skipped$ $±Failures$ $±Errors$
fda-table_38 👶 $+2.76$ $+12$ $+3$ $0$ $0$
Additional test case details
Test Suite $Status$ Time on main $±Time$ Test Case
fda-table_21 👶 $+0.02$ unnamed
fda-table_38 👶 $+1.38$ Table_38_generation_works_with_custom_values
fda-table_38 👶 $+0.52$ Table_38_generation_works_with_default_values
fda-table_38 👶 $+0.85$ Table_38_generation_works_with_risk_difference_column

Results for commit c6ddf2c

♻️ This comment has been updated with latest results.

@edelarua edelarua self-assigned this Feb 20, 2024
@edelarua edelarua self-requested a review February 20, 2024 15:25
Copy link
Collaborator

@edelarua edelarua left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks great!! I just fixed the indentation of one of the labels and added it to the template index so it should be good to go now. Thanks @YoshitoKoujin!

Copy link
Contributor

Unit Tests Summary

  1 files   26 suites   55s ⏱️
102 tests 101 ✅   0 💤 0 ❌ 1 🔥
392 runs  290 ✅ 101 💤 0 ❌ 1 🔥

For more details on these errors, see this check.

Results for commit 539dc2d.

@YoshitoKoujin
Copy link
Collaborator Author

Thank you for your review, @edelarua !

@YoshitoKoujin YoshitoKoujin merged commit 33a5664 into main Feb 23, 2024
20 of 23 checks passed
@YoshitoKoujin YoshitoKoujin deleted the 196-new-table-table-38@main branch February 23, 2024 13:42
huanlugwu added a commit that referenced this pull request May 29, 2024
* 201 new figure figure 14 (#209)

* First draft

First draft (not fully working)

* New push

Now the results are correct. Colors in the table are missing and the order of the group is not correct.

* Delete width= in geom_errorbar

To avoid warning `position_dodge()` requires non-overlapping x intervals

* Update

Put example in comments @examples

* Update fda-fig_14 and argument convention

* tests

Update setup.R to add ggplot2

* quarto page

* _quarto.yml and NEWS.md

* typo

* Put PARAMCD in code mode

* Remove id_var, add visit_var, reverse order of table rows

* [skip actions] Restyle files

* Add to index

* [skip actions] Restyle files

* Empty commit

* Fix unrelated broken template

* [skip actions] Roxygen Man Pages Auto Update

* Empty commit

* Fix lint

* Fix imports/exports

* Update template

---------

Co-authored-by: Emily de la Rua <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>

* 196-new-table-38 (#204)

* 1st commitment for all documents

* [skip actions] Restyle files

* [skip actions] Roxygen Man Pages Auto Update

* Fix table 35 title

* Update index

* Update label indentation

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: Emily de la Rua <[email protected]>

* 195 new table table 36 (#208)

* Add make_table_36

* Add tests for make_table_36

* Addd quarto page for make_table_36

* [skip actions] Restyle files

* Update NEWS file

* Remove scda from table 22

* Solve lintr marks for table 22

* empty commit

* Update WORDLIST

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Abinaya Yogasekaram <[email protected]>
Co-authored-by: ayogasekaram <[email protected]>
Co-authored-by: Emily de la Rua <[email protected]>

* 105 table 09 tplyr (#192)

* Prepare first raw tplyr table including risk difference columns

* Table 9 Tplyr: Update header string in case risk difference columns are expected

* Table 9 Tplyr: Add parameter for overall column

* Tab 9 Tplyr: Introduce soc_var parameter

* Add show_colcounts and prune functionality

* Clean comments

* Replace remaining hard-coded variable names by parameters

* Add option to return a gt_table object

* Add checkmate checks

* Allow for both, character and factor, since tplyr seems to prefer character

* Update roxygen documentation

* Add make_table_09_tplyr() to web page

* Establish first test cases

* Add test for correct column header assignment (make_table_09_tplyr)

* Add column ordering based on arm order for make_table_09_tplyr

* Add final tests and clean

* [skip actions] Restyle files

* Solve lintr markers

* Update after devtools::check()

* [skip actions] Restyle files

* [skip actions] Roxygen Man Pages Auto Update

* Restart github check by code modification

* Update example data frpm scda to random.cdisc.data

* [skip actions] Restyle files

* [skip actions] Roxygen Man Pages Auto Update

* Set RoxygenNote to 7.3.0 as required by GitHub action

* Fix make_table_09_tplyr() row order

* Add scda to 'Suggests' since table 22 still includes it in the example and tests

* Move scda from Suggests to Imports since table 22 quarto page relies on it as well...

* Replace scda w/ random.cdisc.data for table 22 examples and tests

* [skip actions] Roxygen Man Pages Auto Update

* Restrict Tplyr version to <= 1.1.0 until newly introduced incompatibilities w/ higher versions are solved

* Restrict to Tplyr version 1.1.0

* Remove version restriction for Tplyr

* Deactivate risk difference feature until {Tplyr} issue is solved

* Re-document

* [skip style] [skip vbump] Restyle files

---------

Co-authored-by: mattkorb <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: ayogasekaram <[email protected]>

* Update boehringer company logo on website (#214)

* [skip actions] Bump version to 0.1.0.9054

* 211 new table table 33 with gtsummary (#212)

Closes #211

* [skip actions] Bump version to 0.1.0.9055

* 205_BUG_fix _make_table_34 Issue (#215)

* Calculate counts for FMQ levels.
Updated test file and Qualt file accordingly.

* [skip style] [skip vbump] Restyle files

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

* lint R check

* [skip style] [skip vbump] Restyle files

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>

---------

Co-authored-by: Alex Assuied <[email protected]>
Co-authored-by: Emily de la Rua <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: YoshitoKoujin <[email protected]>
Co-authored-by: Korbinian Matthias <[email protected]>
Co-authored-by: Abinaya Yogasekaram <[email protected]>
Co-authored-by: ayogasekaram <[email protected]>
Co-authored-by: Jessica Knizia <[email protected]>
Co-authored-by: mattkorb <[email protected]>
Co-authored-by: edelarua <[email protected]>
huanlugwu added a commit that referenced this pull request Aug 23, 2024
* update branch 207 (#222)

* 201 new figure figure 14 (#209)

* First draft

First draft (not fully working)

* New push

Now the results are correct. Colors in the table are missing and the order of the group is not correct.

* Delete width= in geom_errorbar

To avoid warning `position_dodge()` requires non-overlapping x intervals

* Update

Put example in comments @examples

* Update fda-fig_14 and argument convention

* tests

Update setup.R to add ggplot2

* quarto page

* _quarto.yml and NEWS.md

* typo

* Put PARAMCD in code mode

* Remove id_var, add visit_var, reverse order of table rows

* [skip actions] Restyle files

* Add to index

* [skip actions] Restyle files

* Empty commit

* Fix unrelated broken template

* [skip actions] Roxygen Man Pages Auto Update

* Empty commit

* Fix lint

* Fix imports/exports

* Update template

---------

Co-authored-by: Emily de la Rua <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>

* 196-new-table-38 (#204)

* 1st commitment for all documents

* [skip actions] Restyle files

* [skip actions] Roxygen Man Pages Auto Update

* Fix table 35 title

* Update index

* Update label indentation

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: Emily de la Rua <[email protected]>

* 195 new table table 36 (#208)

* Add make_table_36

* Add tests for make_table_36

* Addd quarto page for make_table_36

* [skip actions] Restyle files

* Update NEWS file

* Remove scda from table 22

* Solve lintr marks for table 22

* empty commit

* Update WORDLIST

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Abinaya Yogasekaram <[email protected]>
Co-authored-by: ayogasekaram <[email protected]>
Co-authored-by: Emily de la Rua <[email protected]>

* 105 table 09 tplyr (#192)

* Prepare first raw tplyr table including risk difference columns

* Table 9 Tplyr: Update header string in case risk difference columns are expected

* Table 9 Tplyr: Add parameter for overall column

* Tab 9 Tplyr: Introduce soc_var parameter

* Add show_colcounts and prune functionality

* Clean comments

* Replace remaining hard-coded variable names by parameters

* Add option to return a gt_table object

* Add checkmate checks

* Allow for both, character and factor, since tplyr seems to prefer character

* Update roxygen documentation

* Add make_table_09_tplyr() to web page

* Establish first test cases

* Add test for correct column header assignment (make_table_09_tplyr)

* Add column ordering based on arm order for make_table_09_tplyr

* Add final tests and clean

* [skip actions] Restyle files

* Solve lintr markers

* Update after devtools::check()

* [skip actions] Restyle files

* [skip actions] Roxygen Man Pages Auto Update

* Restart github check by code modification

* Update example data frpm scda to random.cdisc.data

* [skip actions] Restyle files

* [skip actions] Roxygen Man Pages Auto Update

* Set RoxygenNote to 7.3.0 as required by GitHub action

* Fix make_table_09_tplyr() row order

* Add scda to 'Suggests' since table 22 still includes it in the example and tests

* Move scda from Suggests to Imports since table 22 quarto page relies on it as well...

* Replace scda w/ random.cdisc.data for table 22 examples and tests

* [skip actions] Roxygen Man Pages Auto Update

* Restrict Tplyr version to <= 1.1.0 until newly introduced incompatibilities w/ higher versions are solved

* Restrict to Tplyr version 1.1.0

* Remove version restriction for Tplyr

* Deactivate risk difference feature until {Tplyr} issue is solved

* Re-document

* [skip style] [skip vbump] Restyle files

---------

Co-authored-by: mattkorb <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: ayogasekaram <[email protected]>

* Update boehringer company logo on website (#214)

* [skip actions] Bump version to 0.1.0.9054

* 211 new table table 33 with gtsummary (#212)

Closes #211

* [skip actions] Bump version to 0.1.0.9055

* 205_BUG_fix _make_table_34 Issue (#215)

* Calculate counts for FMQ levels.
Updated test file and Qualt file accordingly.

* [skip style] [skip vbump] Restyle files

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

* lint R check

* [skip style] [skip vbump] Restyle files

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>

---------

Co-authored-by: Alex Assuied <[email protected]>
Co-authored-by: Emily de la Rua <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: YoshitoKoujin <[email protected]>
Co-authored-by: Korbinian Matthias <[email protected]>
Co-authored-by: Abinaya Yogasekaram <[email protected]>
Co-authored-by: ayogasekaram <[email protected]>
Co-authored-by: Jessica Knizia <[email protected]>
Co-authored-by: mattkorb <[email protected]>
Co-authored-by: edelarua <[email protected]>

* with fda-fig_03 added

* [skip style] [skip vbump] Restyle files

* switch from {survminer} to {ggsurvfit}

* [skip style] [skip vbump] Restyle files

* Clean up aesthetics

* Import ggsurvfit

* Update tests

* Refresh template table

* Fix lint

* Fix spelling

* Load data in template

* Use DCSREAS instead of DCTREAS in figure 3 (and table 4)

* Fix R CMD Check note

* Fix remaining documentation

---------

Co-authored-by: Alex Assuied <[email protected]>
Co-authored-by: Emily de la Rua <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: YoshitoKoujin <[email protected]>
Co-authored-by: Korbinian Matthias <[email protected]>
Co-authored-by: Abinaya Yogasekaram <[email protected]>
Co-authored-by: ayogasekaram <[email protected]>
Co-authored-by: Jessica Knizia <[email protected]>
Co-authored-by: mattkorb <[email protected]>
Co-authored-by: edelarua <[email protected]>
Co-authored-by: Emily de la Rua <[email protected]>
huanlugwu added a commit that referenced this pull request Aug 26, 2024
* update branch 207 (#222)

* 201 new figure figure 14 (#209)

* First draft

First draft (not fully working)

* New push

Now the results are correct. Colors in the table are missing and the order of the group is not correct.

* Delete width= in geom_errorbar

To avoid warning `position_dodge()` requires non-overlapping x intervals

* Update

Put example in comments @examples

* Update fda-fig_14 and argument convention

* tests

Update setup.R to add ggplot2

* quarto page

* _quarto.yml and NEWS.md

* typo

* Put PARAMCD in code mode

* Remove id_var, add visit_var, reverse order of table rows

* [skip actions] Restyle files

* Add to index

* [skip actions] Restyle files

* Empty commit

* Fix unrelated broken template

* [skip actions] Roxygen Man Pages Auto Update

* Empty commit

* Fix lint

* Fix imports/exports

* Update template

---------

Co-authored-by: Emily de la Rua <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>

* 196-new-table-38 (#204)

* 1st commitment for all documents

* [skip actions] Restyle files

* [skip actions] Roxygen Man Pages Auto Update

* Fix table 35 title

* Update index

* Update label indentation

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: Emily de la Rua <[email protected]>

* 195 new table table 36 (#208)

* Add make_table_36

* Add tests for make_table_36

* Addd quarto page for make_table_36

* [skip actions] Restyle files

* Update NEWS file

* Remove scda from table 22

* Solve lintr marks for table 22

* empty commit

* Update WORDLIST

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Abinaya Yogasekaram <[email protected]>
Co-authored-by: ayogasekaram <[email protected]>
Co-authored-by: Emily de la Rua <[email protected]>

* 105 table 09 tplyr (#192)

* Prepare first raw tplyr table including risk difference columns

* Table 9 Tplyr: Update header string in case risk difference columns are expected

* Table 9 Tplyr: Add parameter for overall column

* Tab 9 Tplyr: Introduce soc_var parameter

* Add show_colcounts and prune functionality

* Clean comments

* Replace remaining hard-coded variable names by parameters

* Add option to return a gt_table object

* Add checkmate checks

* Allow for both, character and factor, since tplyr seems to prefer character

* Update roxygen documentation

* Add make_table_09_tplyr() to web page

* Establish first test cases

* Add test for correct column header assignment (make_table_09_tplyr)

* Add column ordering based on arm order for make_table_09_tplyr

* Add final tests and clean

* [skip actions] Restyle files

* Solve lintr markers

* Update after devtools::check()

* [skip actions] Restyle files

* [skip actions] Roxygen Man Pages Auto Update

* Restart github check by code modification

* Update example data frpm scda to random.cdisc.data

* [skip actions] Restyle files

* [skip actions] Roxygen Man Pages Auto Update

* Set RoxygenNote to 7.3.0 as required by GitHub action

* Fix make_table_09_tplyr() row order

* Add scda to 'Suggests' since table 22 still includes it in the example and tests

* Move scda from Suggests to Imports since table 22 quarto page relies on it as well...

* Replace scda w/ random.cdisc.data for table 22 examples and tests

* [skip actions] Roxygen Man Pages Auto Update

* Restrict Tplyr version to <= 1.1.0 until newly introduced incompatibilities w/ higher versions are solved

* Restrict to Tplyr version 1.1.0

* Remove version restriction for Tplyr

* Deactivate risk difference feature until {Tplyr} issue is solved

* Re-document

* [skip style] [skip vbump] Restyle files

---------

Co-authored-by: mattkorb <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: ayogasekaram <[email protected]>

* Update boehringer company logo on website (#214)

* [skip actions] Bump version to 0.1.0.9054

* 211 new table table 33 with gtsummary (#212)

Closes #211

* [skip actions] Bump version to 0.1.0.9055

* 205_BUG_fix _make_table_34 Issue (#215)

* Calculate counts for FMQ levels.
Updated test file and Qualt file accordingly.

* [skip style] [skip vbump] Restyle files

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

* lint R check

* [skip style] [skip vbump] Restyle files

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>

---------

Co-authored-by: Alex Assuied <[email protected]>
Co-authored-by: Emily de la Rua <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: YoshitoKoujin <[email protected]>
Co-authored-by: Korbinian Matthias <[email protected]>
Co-authored-by: Abinaya Yogasekaram <[email protected]>
Co-authored-by: ayogasekaram <[email protected]>
Co-authored-by: Jessica Knizia <[email protected]>
Co-authored-by: mattkorb <[email protected]>
Co-authored-by: edelarua <[email protected]>

* with fda-fig_03 added

* [skip style] [skip vbump] Restyle files

* switch from {survminer} to {ggsurvfit}

* [skip style] [skip vbump] Restyle files

* Clean up aesthetics

* Import ggsurvfit

* Update tests

* Refresh template table

* Fix lint

* Fix spelling

* Load data in template

* Use DCSREAS instead of DCTREAS in figure 3 (and table 4)

* Fix R CMD Check note

* Fix remaining documentation

* update cumulative table

* Update test snapshots

---------

Co-authored-by: Alex Assuied <[email protected]>
Co-authored-by: Emily de la Rua <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: YoshitoKoujin <[email protected]>
Co-authored-by: Korbinian Matthias <[email protected]>
Co-authored-by: Abinaya Yogasekaram <[email protected]>
Co-authored-by: ayogasekaram <[email protected]>
Co-authored-by: Jessica Knizia <[email protected]>
Co-authored-by: mattkorb <[email protected]>
Co-authored-by: edelarua <[email protected]>
Co-authored-by: Emily de la Rua <[email protected]>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

[New Table]: Table 38
2 participants