R Under development (unstable) (2024-11-28 r87392 ucrt) -- "Unsuffered Consequences"
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> 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 0 | WARN 1 | SKIP 33 | PASS 439 ]

══ 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'

[ FAIL 0 | WARN 1 | SKIP 33 | PASS 439 ]
> 
> proc.time()
   user  system elapsed 
 240.54   85.04  308.39