R Under development (unstable) (2024-11-28 r87392 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> 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