Last updated on 2024-09-01 11:49:55 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.0.3.8 | 33.57 | 374.67 | 408.24 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.0.3.8 | 27.45 | 226.07 | 253.52 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.0.3.8 | 661.47 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.0.3.8 | 591.21 | ERROR | |||
| r-devel-windows-x86_64 | 0.0.3.8 | 35.00 | 394.00 | 429.00 | ERROR | |
| r-patched-linux-x86_64 | 0.0.3.8 | 35.06 | 341.92 | 376.98 | ERROR | |
| r-release-linux-x86_64 | 0.0.3.8 | 32.24 | 340.85 | 373.09 | ERROR | |
| r-release-macos-arm64 | 0.0.3.8 | 222.00 | OK | |||
| r-release-macos-x86_64 | 0.0.3.8 | 380.00 | OK | |||
| r-release-windows-x86_64 | 0.0.3.8 | 38.00 | 393.00 | 431.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.0.3.8 | 220.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.0.3.8 | 511.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.0.3.8 | 50.00 | 569.00 | 619.00 | ERROR |
Version: 0.0.3.8
Check: tests
Result: ERROR
Running ‘testthat.R’ [212s/203s]
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
------------------------------------------------------------
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
══ Skipped tests (24) ══════════════════════════════════════════════════════════
• On CRAN (24): 'test-data_utils.R:6:3', 'test-data_utils.R:111:3',
'test-data_utils.R:131:3', '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-predict.R:26:3', 'test-predict.R:51:3', 'test-predict.R:108:3',
'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'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-generics.R:25:3'): summary for data_preparation separate=TRUE ──
Error in `print.data.table(data.table(data = object$data), topn = 3, n = 5,
col.names = "none", ...)`: argument 3 matches multiple formal arguments
Backtrace:
▆
1. └─testthat::expect_snapshot(...) at test-generics.R:25:3
2. └─rlang::cnd_signal(state$error)
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.0.3.8
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Getting-Started.Rmd’ using rmarkdown
Quitting from lines 136-137 [unnamed-chunk-2] (Getting-Started.Rmd)
Error: processing vignette 'Getting-Started.Rmd' failed with diagnostics:
argument 3 matches multiple formal arguments
--- failed re-building ‘Getting-Started.Rmd’
SUMMARY: processing the following file failed:
‘Getting-Started.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.0.3.8
Check: tests
Result: ERROR
Running ‘testthat.R’ [122s/145s]
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
------------------------------------------------------------
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
══ Skipped tests (24) ══════════════════════════════════════════════════════════
• On CRAN (24): 'test-data_utils.R:6:3', 'test-data_utils.R:111:3',
'test-data_utils.R:131:3', '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-predict.R:26:3', 'test-predict.R:51:3', 'test-predict.R:108:3',
'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'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-generics.R:25:3'): summary for data_preparation separate=TRUE ──
Error in `print.data.table(data.table(data = object$data), topn = 3, n = 5,
col.names = "none", ...)`: argument 3 matches multiple formal arguments
Backtrace:
▆
1. └─testthat::expect_snapshot(...) at test-generics.R:25:3
2. └─rlang::cnd_signal(state$error)
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.0.3.8
Check: tests
Result: ERROR
Running ‘testthat.R’ [5m/12m]
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
------------------------------------------------------------
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
══ Skipped tests (24) ══════════════════════════════════════════════════════════
• On CRAN (24): 'test-data_utils.R:6:3', 'test-data_utils.R:111:3',
'test-data_utils.R:131:3', '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-predict.R:26:3', 'test-predict.R:51:3', 'test-predict.R:108:3',
'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'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-generics.R:25:3'): summary for data_preparation separate=TRUE ──
Error in `print.data.table(data.table(data = object$data), topn = 3, n = 5,
col.names = "none", ...)`: argument 3 matches multiple formal arguments
Backtrace:
▆
1. └─testthat::expect_snapshot(...) at test-generics.R:25:3
2. └─rlang::cnd_signal(state$error)
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.0.3.8
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Getting-Started.Rmd’ using rmarkdown
Quitting from lines 136-137 [unnamed-chunk-2] (Getting-Started.Rmd)
Error: processing vignette 'Getting-Started.Rmd' failed with diagnostics:
argument 3 matches multiple formal arguments
--- failed re-building ‘Getting-Started.Rmd’
SUMMARY: processing the following file failed:
‘Getting-Started.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 0.0.3.8
Check: tests
Result: ERROR
Running ‘testthat.R’ [276s/322s]
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
------------------------------------------------------------
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
══ Skipped tests (24) ══════════════════════════════════════════════════════════
• On CRAN (24): 'test-data_utils.R:6:3', 'test-data_utils.R:111:3',
'test-data_utils.R:131:3', '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-predict.R:26:3', 'test-predict.R:51:3', 'test-predict.R:108:3',
'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'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-generics.R:25:3'): summary for data_preparation separate=TRUE ──
Error in `print.data.table(data.table(data = object$data), topn = 3, n = 5,
col.names = "none", ...)`: argument 3 matches multiple formal arguments
Backtrace:
▆
1. └─testthat::expect_snapshot(...) at test-generics.R:25:3
2. └─rlang::cnd_signal(state$error)
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.0.3.8
Check: tests
Result: ERROR
Running 'testthat.R' [216s]
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
------------------------------------------------------------
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
══ Skipped tests (24) ══════════════════════════════════════════════════════════
• On CRAN (24): 'test-data_utils.R:6:3', 'test-data_utils.R:111:3',
'test-data_utils.R:131:3', '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-predict.R:26:3', 'test-predict.R:51:3', 'test-predict.R:108:3',
'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'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-generics.R:25:3'): summary for data_preparation separate=TRUE ──
Error in `print.data.table(data.table(data = object$data), topn = 3, n = 5,
col.names = "none", ...)`: argument 3 matches multiple formal arguments
Backtrace:
▆
1. └─testthat::expect_snapshot(...) at test-generics.R:25:3
2. └─rlang::cnd_signal(state$error)
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.0.3.8
Check: tests
Result: ERROR
Running ‘testthat.R’ [188s/241s]
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
------------------------------------------------------------
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
══ Skipped tests (24) ══════════════════════════════════════════════════════════
• On CRAN (24): 'test-data_utils.R:6:3', 'test-data_utils.R:111:3',
'test-data_utils.R:131:3', '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-predict.R:26:3', 'test-predict.R:51:3', 'test-predict.R:108:3',
'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'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-generics.R:25:3'): summary for data_preparation separate=TRUE ──
Error in `print.data.table(data.table(data = object$data), topn = 3, n = 5,
col.names = "none", ...)`: argument 3 matches multiple formal arguments
Backtrace:
▆
1. └─testthat::expect_snapshot(...) at test-generics.R:25:3
2. └─rlang::cnd_signal(state$error)
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.0.3.8
Check: tests
Result: ERROR
Running ‘testthat.R’ [187s/218s]
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
------------------------------------------------------------
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
══ Skipped tests (24) ══════════════════════════════════════════════════════════
• On CRAN (24): 'test-data_utils.R:6:3', 'test-data_utils.R:111:3',
'test-data_utils.R:131:3', '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-predict.R:26:3', 'test-predict.R:51:3', 'test-predict.R:108:3',
'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'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-generics.R:25:3'): summary for data_preparation separate=TRUE ──
Error in `print.data.table(data.table(data = object$data), topn = 3, n = 5,
col.names = "none", ...)`: argument 3 matches multiple formal arguments
Backtrace:
▆
1. └─testthat::expect_snapshot(...) at test-generics.R:25:3
2. └─rlang::cnd_signal(state$error)
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.0.3.8
Check: tests
Result: ERROR
Running 'testthat.R' [207s]
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
------------------------------------------------------------
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
══ Skipped tests (24) ══════════════════════════════════════════════════════════
• On CRAN (24): 'test-data_utils.R:6:3', 'test-data_utils.R:111:3',
'test-data_utils.R:131:3', '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-predict.R:26:3', 'test-predict.R:51:3', 'test-predict.R:108:3',
'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'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-generics.R:25:3'): summary for data_preparation separate=TRUE ──
Error in `print.data.table(data.table(data = object$data), topn = 3, n = 5,
col.names = "none", ...)`: argument 3 matches multiple formal arguments
Backtrace:
▆
1. └─testthat::expect_snapshot(...) at test-generics.R:25:3
2. └─rlang::cnd_signal(state$error)
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.0.3.8
Check: tests
Result: ERROR
Running 'testthat.R' [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
------------------------------------------------------------
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
══ Skipped tests (24) ══════════════════════════════════════════════════════════
• On CRAN (24): 'test-data_utils.R:6:3', 'test-data_utils.R:111:3',
'test-data_utils.R:131:3', '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-predict.R:26:3', 'test-predict.R:51:3', 'test-predict.R:108:3',
'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'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-generics.R:25:3'): summary for data_preparation separate=TRUE ──
Error in `print.data.table(data.table(data = object$data), topn = 3, n = 5,
col.names = "none", ...)`: argument 3 matches multiple formal arguments
Backtrace:
▆
1. └─testthat::expect_snapshot(...) at test-generics.R:25:3
2. └─rlang::cnd_signal(state$error)
[ FAIL 1 | WARN 0 | SKIP 24 | PASS 139 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64