Last updated on 2025-06-07 21:52:08 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.0.4.2 | 43.71 | 595.20 | 638.91 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.0.4.2 | 30.78 | 351.98 | 382.76 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.0.4.2 | 1012.46 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.0.4.2 | 1005.28 | ERROR | |||
| r-devel-windows-x86_64 | 0.0.4.2 | 48.00 | 580.00 | 628.00 | ERROR | |
| r-patched-linux-x86_64 | 0.0.4.2 | 41.60 | 524.10 | 565.70 | ERROR | |
| r-release-linux-x86_64 | 0.0.4.2 | 36.03 | 497.03 | 533.06 | ERROR | |
| r-release-macos-arm64 | 0.0.4.2 | 303.00 | NOTE | |||
| r-release-macos-x86_64 | 0.0.4.2 | 451.00 | OK | |||
| r-release-windows-x86_64 | 0.0.4.2 | 44.00 | 569.00 | 613.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.0.4.2 | 238.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.0.4.2 | 453.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.0.4.2 | 60.00 | 741.00 | 801.00 | ERROR |
Version: 0.0.4.2
Check: DESCRIPTION meta-information
Result: NOTE
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘calculate_weights.Rd’ ‘fit_msm.Rd’ ‘load_expanded_data.Rd’
‘save_to_csv.Rd’ ‘save_to_datatable.Rd’ ‘save_to_duckdb.Rd’
‘set_censor_weight_model.Rd’ ‘set_data.Rd’ ‘set_expansion_options.Rd’
‘set_outcome_model.Rd’ ‘set_switch_weight_model.Rd’
‘weight_model_data_indices.Rd’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-windows-x86_64
Version: 0.0.4.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [320s/329s]
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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.0.4.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [185s/217s]
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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.0.4.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [8m/13m]
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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.0.4.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [8m/19m]
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
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.0.4.2
Check: tests
Result: ERROR
Running 'testthat.R' [317s]
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
Flavor: r-devel-windows-x86_64
Version: 0.0.4.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [284s/332s]
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
Flavor: r-patched-linux-x86_64
Version: 0.0.4.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [266s/303s]
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
Flavor: r-release-linux-x86_64
Version: 0.0.4.2
Check: tests
Result: ERROR
Running 'testthat.R' [308s]
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
Flavor: r-release-windows-x86_64
Version: 0.0.4.2
Check: tests
Result: ERROR
Running 'testthat.R' [391s]
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
Flavor: r-oldrel-windows-x86_64
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