-
Notifications
You must be signed in to change notification settings - Fork 6
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
211 new table table 33 with gtsummary #212
Conversation
Code Coverage Summary
Diff against main
Results for commit: 86ae4d8 Minimum allowed coverage is ♻️ This comment has been updated with latest results |
Unit Test Performance Difference
Additional test case details
Results for commit 1e563e7 ♻️ This comment has been updated with latest results. |
I'm doing a few ajustements on tables 33 and 32. |
Unit Tests Summary 1 files 29 suites 1m 12s ⏱️ Results for commit 86ae4d8. ♻️ This comment has been updated with latest results. |
Handle missing data properly. Use alt_counts_df argument instead of adsl.
…b.com/pharmaverse/falcon into 211-new-table-table-33-with-gtsummary
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Lgtm! I made a few other updates to fix failing tests but your work all looks great. Thanks Alex!!
* 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 <emily.de_la_rua@contractors.roche.com> 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 <emily.de_la_rua@contractors.roche.com> * 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 <73252787+ayogasekaram@users.noreply.github.com> Co-authored-by: ayogasekaram <abinaya.yogasekaram@contractors.roche.com> Co-authored-by: Emily de la Rua <emily.de_la_rua@contractors.roche.com> * 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 <korbinian.matthias@boehringer-ingelheim.com> 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 <abinaya.yogasekaram@contractors.roche.com> * 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 <123543888+aassuied-ps@users.noreply.github.com> Co-authored-by: Emily de la Rua <emily.de_la_rua@contractors.roche.com> 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 <123349854+YoshitoKoujin@users.noreply.github.com> Co-authored-by: Korbinian Matthias <123395522+mattkorb@users.noreply.github.com> Co-authored-by: Abinaya Yogasekaram <73252787+ayogasekaram@users.noreply.github.com> Co-authored-by: ayogasekaram <abinaya.yogasekaram@contractors.roche.com> Co-authored-by: Jessica Knizia <85986258+jknizia@users.noreply.github.com> Co-authored-by: mattkorb <korbinian.matthias@boehringer-ingelheim.com> Co-authored-by: edelarua <edelarua@users.noreply.github.com>
* 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 <emily.de_la_rua@contractors.roche.com> 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 <emily.de_la_rua@contractors.roche.com> * 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 <73252787+ayogasekaram@users.noreply.github.com> Co-authored-by: ayogasekaram <abinaya.yogasekaram@contractors.roche.com> Co-authored-by: Emily de la Rua <emily.de_la_rua@contractors.roche.com> * 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 <korbinian.matthias@boehringer-ingelheim.com> 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 <abinaya.yogasekaram@contractors.roche.com> * 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 <123543888+aassuied-ps@users.noreply.github.com> Co-authored-by: Emily de la Rua <emily.de_la_rua@contractors.roche.com> 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 <123349854+YoshitoKoujin@users.noreply.github.com> Co-authored-by: Korbinian Matthias <123395522+mattkorb@users.noreply.github.com> Co-authored-by: Abinaya Yogasekaram <73252787+ayogasekaram@users.noreply.github.com> Co-authored-by: ayogasekaram <abinaya.yogasekaram@contractors.roche.com> Co-authored-by: Jessica Knizia <85986258+jknizia@users.noreply.github.com> Co-authored-by: mattkorb <korbinian.matthias@boehringer-ingelheim.com> Co-authored-by: edelarua <edelarua@users.noreply.github.com> * 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 <123543888+aassuied-ps@users.noreply.github.com> Co-authored-by: Emily de la Rua <emily.de_la_rua@contractors.roche.com> 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 <123349854+YoshitoKoujin@users.noreply.github.com> Co-authored-by: Korbinian Matthias <123395522+mattkorb@users.noreply.github.com> Co-authored-by: Abinaya Yogasekaram <73252787+ayogasekaram@users.noreply.github.com> Co-authored-by: ayogasekaram <abinaya.yogasekaram@contractors.roche.com> Co-authored-by: Jessica Knizia <85986258+jknizia@users.noreply.github.com> Co-authored-by: mattkorb <korbinian.matthias@boehringer-ingelheim.com> Co-authored-by: edelarua <edelarua@users.noreply.github.com> Co-authored-by: Emily de la Rua <59304861+edelarua@users.noreply.github.com>
* 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 <emily.de_la_rua@contractors.roche.com> 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 <emily.de_la_rua@contractors.roche.com> * 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 <73252787+ayogasekaram@users.noreply.github.com> Co-authored-by: ayogasekaram <abinaya.yogasekaram@contractors.roche.com> Co-authored-by: Emily de la Rua <emily.de_la_rua@contractors.roche.com> * 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 <korbinian.matthias@boehringer-ingelheim.com> 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 <abinaya.yogasekaram@contractors.roche.com> * 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 <123543888+aassuied-ps@users.noreply.github.com> Co-authored-by: Emily de la Rua <emily.de_la_rua@contractors.roche.com> 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 <123349854+YoshitoKoujin@users.noreply.github.com> Co-authored-by: Korbinian Matthias <123395522+mattkorb@users.noreply.github.com> Co-authored-by: Abinaya Yogasekaram <73252787+ayogasekaram@users.noreply.github.com> Co-authored-by: ayogasekaram <abinaya.yogasekaram@contractors.roche.com> Co-authored-by: Jessica Knizia <85986258+jknizia@users.noreply.github.com> Co-authored-by: mattkorb <korbinian.matthias@boehringer-ingelheim.com> Co-authored-by: edelarua <edelarua@users.noreply.github.com> * 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 <123543888+aassuied-ps@users.noreply.github.com> Co-authored-by: Emily de la Rua <emily.de_la_rua@contractors.roche.com> 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 <123349854+YoshitoKoujin@users.noreply.github.com> Co-authored-by: Korbinian Matthias <123395522+mattkorb@users.noreply.github.com> Co-authored-by: Abinaya Yogasekaram <73252787+ayogasekaram@users.noreply.github.com> Co-authored-by: ayogasekaram <abinaya.yogasekaram@contractors.roche.com> Co-authored-by: Jessica Knizia <85986258+jknizia@users.noreply.github.com> Co-authored-by: mattkorb <korbinian.matthias@boehringer-ingelheim.com> Co-authored-by: edelarua <edelarua@users.noreply.github.com> Co-authored-by: Emily de la Rua <59304861+edelarua@users.noreply.github.com>
Closes #211