Running ‘testthat.R’ [8m/10m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(TrialEmulation)
  > 
  > data.table::setDTthreads(2)
  > test_check("TrialEmulation")
  Starting data manipulation
  Starting data extension
  Summary of extended data:
  Number of observations: 1939053
  ------------------------------------------------------------
  
  Starting data manipulation
  P(treatment = 1 | previous treatment = 0) for denominator
  
  Call:
  glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
      data = data)
  
  Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
  (Intercept) -3.84325    0.04785  -80.31   <2e-16 ***
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  (Dispersion parameter for binomial family taken to be 1)
  
      Null deviance: 4329.7  on 21263  degrees of freedom
  Residual deviance: 4329.7  on 21263  degrees of freedom
  AIC: 4331.7
  
  Number of Fisher Scoring iterations: 6
  
  P(treatment = 1 | previous treatment = 0) for numerator
  
  Call:
  glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
      data = data)
  
  Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
  (Intercept) -3.84325    0.04785  -80.31   <2e-16 ***
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  (Dispersion parameter for binomial family taken to be 1)
  
      Null deviance: 4329.7  on 21263  degrees of freedom
  Residual deviance: 4329.7  on 21263  degrees of freedom
  AIC: 4331.7
  
  Number of Fisher Scoring iterations: 6
  
  P(treatment = 1 | previous treatment = 1) for denominator
  
  Call:
  glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
      data = data)
  
  Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
  (Intercept)  4.37616    0.06815   64.21   <2e-16 ***
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  (Dispersion parameter for binomial family taken to be 1)
  
      Null deviance: 2346.7  on 17555  degrees of freedom
  Residual deviance: 2346.7  on 17555  degrees of freedom
  AIC: 2348.7
  
  Number of Fisher Scoring iterations: 7
  
  P(treatment = 1 | previous treatment = 1) for numerator
  
  Call:
  glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
      data = data)
  
  Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
  (Intercept)  4.37616    0.06815   64.21   <2e-16 ***
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  (Dispersion parameter for binomial family taken to be 1)
  
      Null deviance: 2346.7  on 17555  degrees of freedom
  Residual deviance: 2346.7  on 17555  degrees of freedom
  AIC: 2348.7
  
  Number of Fisher Scoring iterations: 7
  
  Starting data extension
  Summary of extended data:
  Number of observations: 963883
  ------------------------------------------------------------
  
  Starting data manipulation
  P(treatment = 1 | previous treatment = 0) for denominator
  
  Call:
  glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
      data = data)
  
  Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
  (Intercept) -3.32517    0.03599   -92.4   <2e-16 ***
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  (Dispersion parameter for binomial family taken to be 1)
  
      Null deviance: 6948.7  on 23042  degrees of freedom
  Residual deviance: 6948.7  on 23042  degrees of freedom
  AIC: 6950.7
  
  Number of Fisher Scoring iterations: 6
  
  P(treatment = 1 | previous treatment = 0) for numerator
  
  Call:
  glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
      data = data)
  
  Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
  (Intercept) -3.32517    0.03599   -92.4   <2e-16 ***
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  (Dispersion parameter for binomial family taken to be 1)
  
      Null deviance: 6948.7  on 23042  degrees of freedom
  Residual deviance: 6948.7  on 23042  degrees of freedom
  AIC: 6950.7
  
  Number of Fisher Scoring iterations: 6
  
  P(treatment = 1 | previous treatment = 1) for denominator
  
  Call:
  glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
      data = data)
  
  Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
  (Intercept)   3.9124     0.0453   86.37   <2e-16 ***
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  (Dispersion parameter for binomial family taken to be 1)
  
      Null deviance: 4892.8  on 25356  degrees of freedom
  Residual deviance: 4892.8  on 25356  degrees of freedom
  AIC: 4894.8
  
  Number of Fisher Scoring iterations: 6
  
  P(treatment = 1 | previous treatment = 1) for numerator
  
  Call:
  glm(formula = treatment ~ 1, family = binomial(link = "logit"), 
      data = data)
  
  Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
  (Intercept)   3.9124     0.0453   86.37   <2e-16 ***
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  (Dispersion parameter for binomial family taken to be 1)
  
      Null deviance: 4892.8  on 25356  degrees of freedom
  Residual deviance: 4892.8  on 25356  degrees of freedom
  AIC: 4894.8
  
  Number of Fisher Scoring iterations: 6
  
  Starting data extension
  Summary of extended data:
  Number of observations: 1939053
  ------------------------------------------------------------
  
  Starting data manipulation
  P(treatment = 1 | previous treatment = 0) for denominator
  
  Call:
  glm(formula = treatment ~ age_s + x4 + x2 + x1, family = binomial(link = "logit"), 
      data = data)
  
  Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
  (Intercept) -0.13699    0.25792  -0.531   0.5953    
  age_s       -0.04014    0.19890  -0.202   0.8401    
  x4           1.09583    0.21355   5.131 2.88e-07 ***
  x2           0.09687    0.19430   0.499   0.6181    
  x1           0.61385    0.36325   1.690   0.0911 .  
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  (Dispersion parameter for binomial family taken to be 1)
  
      Null deviance: 232.27  on 169  degrees of freedom
  Residual deviance: 185.41  on 165  degrees of freedom
  AIC: 195.41
  
  Number of Fisher Scoring iterations: 4
  
  P(treatment = 1 | previous treatment = 0) for numerator
  
  Call:
  glm(formula = treatment ~ age_s + x4, family = binomial(link = "logit"), 
      data = data)
  
  Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
  (Intercept)  0.12031    0.20308   0.592    0.554    
  age_s        0.01215    0.19512   0.062    0.950    
  x4           1.10863    0.21415   5.177 2.26e-07 ***
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  (Dispersion parameter for binomial family taken to be 1)
  
      Null deviance: 232.27  on 169  degrees of freedom
  Residual deviance: 188.62  on 167  degrees of freedom
  AIC: 194.62
  
  Number of Fisher Scoring iterations: 4
  
  P(treatment = 1 | previous treatment = 1) for denominator
  
  Call:
  glm(formula = treatment ~ age_s + x4 + x2 + x1, family = binomial(link = "logit"), 
      data = data)
  
  Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
  (Intercept)   0.6783     0.2797   2.425 0.015318 *  
  age_s        -0.1924     0.2115  -0.910 0.362887    
  x4            0.8536     0.2218   3.849 0.000119 ***
  x2            0.3246     0.1963   1.653 0.098252 .  
  x1            0.7923     0.4914   1.612 0.106867    
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  (Dispersion parameter for binomial family taken to be 1)
  
      Null deviance: 188.83  on 150  degrees of freedom
  Residual deviance: 164.85  on 146  degrees of freedom
  AIC: 174.85
  
  Number of Fisher Scoring iterations: 4
  
  P(treatment = 1 | previous treatment = 1) for numerator
  
  Call:
  glm(formula = treatment ~ age_s + x4, family = binomial(link = "logit"), 
      data = data)
  
  Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
  (Intercept)   0.7476     0.2520   2.967 0.003011 ** 
  age_s        -0.1686     0.2081  -0.810 0.417888    
  x4            0.7935     0.2163   3.669 0.000244 ***
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  (Dispersion parameter for binomial family taken to be 1)
  
      Null deviance: 188.83  on 150  degrees of freedom
  Residual deviance: 170.78  on 148  degrees of freedom
  AIC: 176.78
  
  Number of Fisher Scoring iterations: 4
  
  Starting data extension
  Summary of extended data:
  Number of observations: 500
  ------------------------------------------------------------
  
  [ FAIL 2 | WARN 1 | SKIP 33 | PASS 437 ]
  
  ══ Skipped tests (33) ══════════════════════════════════════════════════════════
  • On CRAN (33): 'test-data_utils.R:6:3', 'test-data_utils.R:111:3',
    'test-data_utils.R:131:3', 'test-generics.R:25:3', 'test-generics.R:66:3',
    'test-generics.R:95:3', 'test-modelling.R:99:3', 'test-modelling.R:154:3',
    'test-modelling.R:175:3', 'test-modelling.R:205:3', 'test-modelling.R:229:3',
    'test-modelling.R:266:3', 'test-modelling.R:290:3', 'test-modelling.R:314:3',
    'test-modelling.R:357:3', 'test-modelling.R:431:3', 'test-predict.R:26:3',
    'test-predict.R:51:3', 'test-predict.R:108:3', 'test-predict.R:171:3',
    'test-sampling.R:5:3', 'test-sampling.R:15:3', 'test-sampling.R:34:3',
    'test-sampling.R:54:3', 'test-sampling.R:86:3', 'test-sampling.R:103:3',
    'test-sampling.R:180:3', 'test-te_weights.R:20:3', 'test-te_weights.R:62:3',
    'test-trial_sequence.R:41:3', 'test-trial_sequence.R:45:3',
    'test-trial_sequence.R:49:3', 'test-trial_sequence.R:56:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-te_datastore_duckdb.R:115:3'): sample_controls works with trial_sequence objects containing te_datastore_duckdb objects ──
  sort(sc_04@outcome_data@data$id) (`actual`) not equal to c(...) (`expected`).
  
    `actual[1:14]`: 2 16 20 21 44 44 44 44 44 47 and 4 more...
  `expected[1:11]`:   16 20    44 44 44 44 44 49           ...
  
    `actual[18:28]`: 59 59 59 65 70 70       74 74 and 4 more...
  `expected[15:28]`: 59 59 59 59 59 60 60 60 74 74           ...
  ── Failure ('test-te_datastore_duckdb.R:201:3'): load_expanded_data works with trial_sequence objects containing te_datastore_duckdb objects ──
  sort(sc_04@outcome_data@data$id) (`actual`) not equal to c(...) (`expected`).
  
    `actual[1:14]`: 2 16 20 21 44 44 44 44 44 47 and 4 more...
  `expected[1:11]`:   16 20    44 44 44 44 44 49           ...
  
    `actual[18:28]`: 59 59 59 65 70 70       74 74 and 4 more...
  `expected[15:28]`: 59 59 59 59 59 60 60 60 74 74           ...
  
  [ FAIL 2 | WARN 1 | SKIP 33 | PASS 437 ]
  Error: Test failures
  Execution halted