tests/testthat/_snaps/logistic_regression.md

In tern: Create Common TLGs Used in Clinical Trials

tidy.glm works as expected for simple case

Code
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Output
    variable   variable_label  term              term_label interaction
  1    ARMCD Planned Arm Code ARM A Reference ARM A, n = 64            
  2    ARMCD Planned Arm Code ARM B           ARM B, n = 68            
  3    ARMCD Planned Arm Code ARM C           ARM C, n = 52            
  4      AGE              Age   AGE                     Age            
  5      SEX              Sex     F    Reference F, n = 100            
  6      SEX              Sex     M               M, n = 84            
    interaction_label reference reference_label  estimate  std_error df
  1                                                                   2
  2                                             -1.973924    1.14659  1
  3                                              16.01132     2300.5  1
  4                                             0.1674111 0.08943489  1
  5                                                                    
  6                                             0.6291583  0.9193781  1
        pvalue is_variable_summary is_term_summary odds_ratio        lcl      ucl
  1  0.2272022                TRUE           FALSE                               
  2  0.0851491               FALSE            TRUE  0.1389107 0.00724572 2.663113
  3  0.9944468               FALSE            TRUE    8987294          0      Inf
  4 0.06122358               FALSE            TRUE    1.18224   0.938983 1.488517
  5                           TRUE           FALSE                               
  6  0.4937666               FALSE            TRUE   1.876031  0.1756955 20.03177
                        ci
  1                       
  2 0.00724572, 2.66311277
  3                 0, Inf
  4     0.938983, 1.488517
  5                       
  6  0.1756955, 20.0317685

tidy.glm works as expected for interaction case

Code
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Output
      variable  term interaction reference   estimate std_error
  1        SEX     F                                           
  2        SEX     M                        0.7437057 0.9406595
  3      ARMCD ARM A                                           
  4      ARMCD ARM B                        -11.53157  6.443318
  5      ARMCD ARM B         AGE        35         NA        NA
  6      ARMCD ARM C                         14.72268  13103.52
  7      ARMCD ARM C         AGE        35         NA        NA
  8        AGE   AGE                       -0.0511774 0.1462201
  9        AGE   AGE       ARMCD     ARM A         NA        NA
  10       AGE   AGE       ARMCD     ARM B         NA        NA
  11       AGE   AGE       ARMCD     ARM C         NA        NA
  12 ARMCD:AGE ARM A                                           
  13 ARMCD:AGE ARM B                        0.3040042 0.1882037
  14 ARMCD:AGE ARM C                       0.04825293  356.2659

logistic_regression_cols works as expected

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Output
     Degrees of Freedom   Parameter Estimate   Standard Error   Odds Ratio   Wald 75% CI   p-value
  ————————————————————————————————————————————————————————————————————————————————————————————————
             df                estimate              se             or           ci           p

summarize_logistic works as expected for interaction model with continuous variable

Code
  res
Output
                                          Degrees of Freedom   Parameter Estimate   Standard Error   Odds Ratio     Wald 99% CI     p-value
  —————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
  Sex                                                                                                                                      
    Reference F, n = 100                                                                                                                   
    M, n = 84                                     1                  0.744              0.941           2.10       (0.19, 23.73)    0.4292 
  Planned Arm Code                                2                                                                                 0.2016 
    Reference ARM A, n = 64                                                                                                                
    ARM B, n = 68                                 1                 -11.532             6.443                                       0.0735 
      Age                                                                                                                                  
        35                                                                                              0.41       (0.01, 11.60)           
    ARM C, n = 52                                 1                  14.723           13103.521                                     0.9991 
      Age                                                                                                                                  
        35                                                                                            >999.99     (0.00, >999.99)          
  Age                                                                                                                                      
    Age                                           1                  -0.051             0.146                                       0.7263 
      Planned Arm Code                                                                                                                     
        ARM A                                                                                           0.95       (0.65, 1.38)            
        ARM B                                                                                           1.29       (0.95, 1.75)            
        ARM C                                                                                           1.00      (0.00, >999.99)          
  Interaction of Planned Arm Code * Age           2                                                                                 0.2713 
    Reference ARM A, n = 64                                                                                                                
    ARM B, n = 68                                 1                  0.304              0.188                                       0.1062 
    ARM C, n = 52                                 1                  0.048             356.266                                      0.9999

summarize_logistic works as expected for interaction model with categorical variable

Code
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Output
                                          Degrees of Freedom   Parameter Estimate   Standard Error   Odds Ratio     Wald 99% CI     p-value
  —————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
  Age                                                                                                                                      
    Age                                           1                  0.186              0.093           1.21       (0.95, 1.53)     0.0461 
  Planned Arm Code                                2                                                                                 1.0000 
    Reference ARM A, n = 64                                                                                                                
    ARM B, n = 68                                 1                 -19.927            4655.091                                     0.9966 
      Sex                                                                                                                                  
        F                                                                                               0.00      (0.00, >999.99)          
        M                                                                                               1.05       (0.02, 45.12)           
    ARM C, n = 52                                 1                  -0.485            6977.551                                     0.9999 
      Sex                                                                                                                                  
        F                                                                                               0.62      (0.00, >999.99)          
        M                                                                                             >999.99     (0.00, >999.99)          
  Sex                                                                                                                                      
    Reference F, n = 100                                                                                                                   
    M, n = 84                                     1                 -18.467            4655.091                                     0.9968 
      Planned Arm Code                                                                                                                     
        ARM A                                                                                           0.00      (0.00, >999.99)          
        ARM B                                                                                           4.52       (0.22, 94.89)           
        ARM C                                                                                           1.20      (0.00, >999.99)          
  Interaction of Planned Arm Code * Sex           2                                                                                 1.0000 
    Reference ARM A or F, n = 129                                                                                                          
    ARM B * M, n = 31                             1                  19.975            4655.091                                     0.9966 
    ARM C * M, n = 24                             1                  18.649            8840.154                                     0.9983

summarize_logistic works as expected for simple model without interactions

Code
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Output
                              Degrees of Freedom   Parameter Estimate   Standard Error   Odds Ratio     Wald 99% CI     p-value
  —————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
  Planned Arm Code                    2                                                                                 0.2435 
    Reference ARM A, n = 64                                                                                                    
    ARM B, n = 68                     1                  -1.905             1.134           0.15       (<0.01, 2.76)    0.0928 
    ARM C, n = 52                     1                  16.089            2306.294       >999.99     (0.00, >999.99)   0.9944 
  Age                                                                                                                          
    Age                               1                  0.165              0.090           1.18       (0.94, 1.49)     0.0665

tern documentation built on Sept. 24, 2024, 9:06 a.m.