insightsengineering / tlg-catalog

A catalog of Tables, Listings and Graphs (TLGs) created with NEST R packages
https://insightsengineering.github.io/tlg-catalog/
Other
20 stars 8 forks source link

Fix failing integration tests #240

Closed edelarua closed 7 months ago

edelarua commented 7 months ago
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-tables-efficacy-mmrmt01.R:1:1'): tables/efficacy/mmrmt01.qmd result_v1 stable ──
  Snapshot of code has changed (variant 'stable'):
  old[11:17] vs new[11:17]
        Difference in Adjusted Means (SE)                       0.759 (0.973)      -0.325 (0.976) 
          95% CI                                               (-1.155, 2.672)    (-2.243, 1.593) 
          Relative Increase (%)                                     21.8%              -9.3%      
  -       p-value (MMRM)                                            0.4362             0.7394     
  +       p-value (MMRM)                                            0.4362             0.7393     
      WEEK 2 DAY 15                                                                               
        n                                         134                134                132       
        Adjusted Mean (SE)                   9.135 (0.768)      9.018 (0.767)      8.509 (0.773)  

  old[19:25] vs new[19:25]
        Difference in Adjusted Means (SE)                       -0.117 (1.087)     -0.626 (1.090) 
          95% CI                                               (-2.253, 2.020)    (-2.768, 1.517) 
          Relative Increase (%)                                     -1.3%              -6.8%      
  -       p-value (MMRM)                                            0.9146             0.5662     
  +       p-value (MMRM)                                            0.9147             0.5662     
      WEEK 3 DAY 22                                                                               
        n                                         134                134                132       
        Adjusted Mean (SE)                   13.547 (0.871)     16.014 (0.871)     15.789 (0.877) 

  * Run `testthat::snapshot_accept('stable/tables-efficacy-mmrmt01')` to accept the change.
  * Run `testthat::snapshot_review('stable/tables-efficacy-mmrmt01')` to interactively review the change.
  ── Failure ('test-tables-efficacy-rbmit01.R:1:1'): tables/efficacy/rbmit01.qmd result_v1 stable ──
  Snapshot of code has changed (variant 'stable'):
  old[11:33] vs new[11:33]
          Relative Reduction (%)                                     5.7%      
          p-value (RBMI)                                            0.8932     
      5                                                                        
  -     Adjusted Mean (SE)                   -4.247 (0.649)     -2.815 (0.646) 
  +     Adjusted Mean (SE)                   -4.261 (0.646)     -2.814 (0.643) 
  -       95% CI                            (-5.527, -2.966)   (-4.091, -1.540)
  +       95% CI                            (-5.537, -2.984)   (-4.084, -1.545)
  -     Difference in Adjusted Means (SE)                       1.431 (0.915)  
  +     Difference in Adjusted Means (SE)                       1.447 (0.915)  
  -       95% CI                                               (-0.377, 3.239) 
  +       95% CI                                               (-0.360, 3.254) 
  -       Relative Reduction (%)                                    -33.7%     
  +       Relative Reduction (%)                                    -34.0%     
  -       p-value (RBMI)                                            0.1200     
  +       p-value (RBMI)                                            0.1159     
      6                                                                        
  -     Adjusted Mean (SE)                   -6.388 (0.724)     -4.115 (0.692) 
  +     Adjusted Mean (SE)                   -6.365 (0.721)     -4.123 (0.689) 
  -       95% CI                            (-7.820, -4.956)   (-5.481, -2.748)
  +       95% CI                            (-7.791, -4.939)   (-5.484, -2.761)
  -     Difference in Adjusted Means (SE)                       2.274 (1.005)  
  +     Difference in Adjusted Means (SE)                       2.242 (0.998)  
  -       95% CI                                                (0.287, 4.261) 
  +       95% CI                                                (0.269, 4.216) 
  -       Relative Reduction (%)                                    -35.6%     
  +       Relative Reduction (%)                                    -35.2%     
  -       p-value (RBMI)                                            0.0252     
  +       p-value (RBMI)                                            0.0262     
      7                                                                        
  -     Adjusted Mean (SE)                   -7.649 (0.792)     -4.812 (0.764) 
  +     Adjusted Mean (SE)                   -7.665 (0.831)     -4.802 (0.762) 
  -       95% CI                            (-9.217, -6.081)   (-6.323, -3.301)
  +       95% CI                            (-9.314, -6.017)   (-6.308, -3.296)
  -     Difference in Adjusted Means (SE)                       2.836 (1.121)  
  +     Difference in Adjusted Means (SE)                       2.863 (1.120)  
  -       95% CI                                                (0.617, 5.056) 
  +       95% CI                                                (0.645, 5.082) 
  -       Relative Reduction (%)                                    -37.1%     
  +       Relative Reduction (%)                                    -37.4%     
  -       p-value (RBMI)                                            0.0127     
  +       p-value (RBMI)                                            0.0118     

  * Run `testthat::snapshot_accept('stable/tables-efficacy-rbmit01')` to accept the change.
  * Run `testthat::snapshot_review('stable/tables-efficacy-rbmit01')` to interactively review the change.
  ── Failure ('test-tables-efficacy-ttet01.R:1:1'): tables/efficacy/ttet01.qmd result_v4 stable ──
  Snapshot of code has changed (variant 'stable'):
  old[18:26] vs new[18:26]
        Hazard Ratio                                           1.00              1.29      
        95% CI                                             (0.69, 1.44)      (0.91, 1.83)  
      Stratified Analysis                                                                  
  -     p-value (log-rank)                                    0.9998            0.1541     
  +     p-value (log-rank)                                    0.9978            0.1733     
  -     Hazard Ratio                                           1.00              1.29      
  +     Hazard Ratio                                           1.00              1.27      
  -     95% CI                                             (0.69, 1.44)      (0.91, 1.83)  
  +     95% CI                                             (0.69, 1.44)      (0.90, 1.81)  
      12 Months                                                                            
        Patients remaining at risk            49                48                37       
        Event Free Rate (%)                  56.72             56.72             47.73     

  * Run `testthat::snapshot_accept('stable/tables-efficacy-ttet01')` to accept the change.
  * Run `testthat::snapshot_review('stable/tables-efficacy-ttet01')` to interactively review the change.
  ── Failure ('test-tables-lab-results-lbt11_bl.R:1:1'): tables/lab-results/lbt11_bl.qmd result_v3 stable ──
  Snapshot of code has changed (variant 'stable'):
  old[16:24] vs new[16:24]
        Hazard Ratio                                            1.27               0.84      
        95% CI                                              (0.63, 2.56)       (0.40, 1.75)  
      Stratified By: RACE, SEX                                                               
  -     p-value (log-rank)                                     0.5013             0.6413     
  +     p-value (log-rank)                                     0.3886             0.7970     
  -     Hazard Ratio                                            1.27               0.84      
  +     Hazard Ratio                                            1.39               0.91      
  -     95% CI                                              (0.63, 2.56)       (0.40, 1.75)  
  +     95% CI                                              (0.65, 2.97)       (0.43, 1.93)  
      ———————————————————————————————————————————————————————————————————————————————————————

      {1} - Censored observations: range minimum & maximum

  * Run `testthat::snapshot_accept('stable/tables-lab-results-lbt11_bl')` to accept the change.
  * Run `testthat::snapshot_review('stable/tables-lab-results-lbt11_bl')` to interactively review the change.
  ── Failure ('test-tables-lab-results-lbt11.R:1:1'): tables/lab-results/lbt11.qmd result_v3 stable ──
  Snapshot of code has changed (variant 'stable'):
  old[16:24] vs new[16:24]
        Hazard Ratio                                            0.43               0.58      
        95% CI                                              (0.19, 0.94)       (0.26, 1.27)  
      Stratified By: RACE, SEX                                                               
  -     p-value (log-rank)                                     0.0295             0.1687     
  +     p-value (log-rank)                                     0.0858             0.1605     
  -     Hazard Ratio                                            0.43               0.58      
  +     Hazard Ratio                                            0.51               0.57      
  -     95% CI                                              (0.19, 0.94)       (0.26, 1.27)  
  +     95% CI                                              (0.23, 1.12)       (0.26, 1.26)  
      ———————————————————————————————————————————————————————————————————————————————————————

      {1} - Censored observations: range minimum & maximum

  * Run `testthat::snapshot_accept('stable/tables-lab-results-lbt11')` to accept the change.
  * Run `testthat::snapshot_review('stable/tables-lab-results-lbt11')` to interactively review the change.

  [ FAIL 5 | WARN 0 | SKIP 88 | PASS 247 ]