Last updated on 2022-09-11 12:56:27 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2022.03.22 | 293.44 | 519.11 | 812.55 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2022.03.22 | 229.97 | 364.12 | 594.09 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2022.03.22 | 1027.77 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 2022.03.22 | 1002.38 | ERROR | |||
| r-devel-windows-x86_64 | 2022.03.22 | 552.00 | 553.00 | 1105.00 | ERROR | |
| r-patched-linux-x86_64 | 2022.03.22 | 244.49 | 458.65 | 703.14 | ERROR | |
| r-release-linux-x86_64 | 2022.03.22 | 200.30 | 459.43 | 659.73 | ERROR | |
| r-release-macos-arm64 | 2022.03.22 | 227.00 | NOTE | |||
| r-release-macos-x86_64 | 2022.03.22 | 387.00 | NOTE | |||
| r-release-windows-x86_64 | 2022.03.22 | 464.00 | 544.00 | 1008.00 | ERROR | |
| r-oldrel-macos-arm64 | 2022.03.22 | 230.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 2022.03.22 | 287.00 | NOTE | |||
| r-oldrel-windows-ix86+x86_64 | 2022.03.22 | 703.00 | 848.00 | 1551.00 | ERROR |
Version: 2022.03.22
Check: tests
Result: ERROR
Running 'test-AUC.R' [8s/10s]
Running 'test-BinomialRegression.R' [10s/13s]
Running 'test-BrierScore.R' [10s/11s]
Running 'test-CauseSpecificCoxRegression.R' [10s/12s]
Running 'test-FineGrayRegression.R' [7s/9s]
Running 'test-boxplotScore.R' [8s/8s]
Running 'test-iidCox.R' [10s/12s]
Running 'test-phreg.R' [13s/15s]
Running 'test-predictCox.R' [25s/26s]
Running 'test-predictCoxPL.R' [9s/11s]
Running 'test-predictRisk-TD.R' [10s/11s]
Running 'test-predictRisk.R' [10s/11s]
Running 'test-score-bootstrap.R' [31s/36s]
Running 'test-score.R' [20s/17s]
Running 'test-summary-score.R' [18s/16s]
Running 'test-wglm.R' [9s/11s]
Running the tests in 'tests/test-wglm.R' failed.
Complete output:
> ### test-wglm.R ---
> ##----------------------------------------------------------------------
> ## Author: Brice Ozenne
> ## Created: Dec 21 2021 (11:04)
> ## Version:
> ## Last-Updated: Dec 21 2021 (16:46)
> ## By: Brice Ozenne
> ## Update #: 16
> ##----------------------------------------------------------------------
> ##
> ### Commentary:
> ##
> ### Change Log:
> ##----------------------------------------------------------------------
> ##
> ### Code:
>
> ## * Packages
> library(testthat)
> library(data.table)
> library(mets)
Loading required package: timereg
Loading required package: survival
Loading required package: lava
Attaching package: 'lava'
The following object is masked from 'package:testthat':
compare
mets version 1.3.0
> library(riskRegression)
riskRegression version 2022.03.22
> library(survival)
>
> ## * Simulate data
> set.seed(10)
> n <- 250
> tau <- 1:5
> d <- sampleData(n, outcome = "competing.risks")
> dFull <- d[event!=0] ## remove censoring
> dSurv <- d[event!=2] ## remove competing risk
>
> ## * no censoring
> test_that("wglm - no censoring",{
+ test <- wglm(regressor.event = ~ X1 + X8, formula.censor = Surv(time,event==0) ~ 1,
+ times = tau, data = dFull)
+
+ GS <- suppressWarnings(logitIPCW(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull))
+
+ expect_equal(coef(test, time = tau[5]), summary(GS)$coef[,"Estimate"], tol = 1e-5)
+ expect_equal(summary(test, print = FALSE)[[5]][,"Std. Error"], summary(GS)$coef[,"Std.Err"], tol = 1e-5)
+
+ ## ate
+ test.ate <- ate(test, data = dFull, times = tau, treatment = "X1", verbose = FALSE)
+ GS.ate <- logitATE(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull, treat.model = X1~1)
+ expect_equal(test.ate$diffRisk[5,estimate], GS.ate$difriskG, tol = 1e-5)
+ expect_equal(test.ate$diffRisk[5,se], GS.ate$se.difriskG, tol = 1e-5)
+ })
-- Failure (???): wglm - no censoring ------------------------------------------
test.ate$diffRisk[5, estimate] not equal to GS.ate$difriskG.
names for current but not for target
Error in reporter$stop_if_needed() : Test failed
Calls: test_that -> <Anonymous>
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2022.03.22
Check: tests
Result: ERROR
Running ‘test-AUC.R’ [6s/11s]
Running ‘test-BinomialRegression.R’ [7s/11s]
Running ‘test-BrierScore.R’ [7s/11s]
Running ‘test-CauseSpecificCoxRegression.R’ [7s/11s]
Running ‘test-FineGrayRegression.R’ [5s/9s]
Running ‘test-boxplotScore.R’ [5s/8s]
Running ‘test-iidCox.R’ [7s/10s]
Running ‘test-phreg.R’ [9s/16s]
Running ‘test-predictCox.R’ [16s/24s]
Running ‘test-predictCoxPL.R’ [6s/10s]
Running ‘test-predictRisk-TD.R’ [7s/12s]
Running ‘test-predictRisk.R’ [7s/10s]
Running ‘test-score-bootstrap.R’ [21s/32s]
Running ‘test-score.R’ [12s/19s]
Running ‘test-summary-score.R’ [10s/15s]
Running ‘test-wglm.R’ [6s/10s]
Running the tests in ‘tests/test-wglm.R’ failed.
Complete output:
> ### test-wglm.R ---
> ##----------------------------------------------------------------------
> ## Author: Brice Ozenne
> ## Created: Dec 21 2021 (11:04)
> ## Version:
> ## Last-Updated: Dec 21 2021 (16:46)
> ## By: Brice Ozenne
> ## Update #: 16
> ##----------------------------------------------------------------------
> ##
> ### Commentary:
> ##
> ### Change Log:
> ##----------------------------------------------------------------------
> ##
> ### Code:
>
> ## * Packages
> library(testthat)
> library(data.table)
> library(mets)
Loading required package: timereg
Loading required package: survival
Loading required package: lava
Attaching package: 'lava'
The following object is masked from 'package:testthat':
compare
mets version 1.3.0
> library(riskRegression)
riskRegression version 2022.03.22
> library(survival)
>
> ## * Simulate data
> set.seed(10)
> n <- 250
> tau <- 1:5
> d <- sampleData(n, outcome = "competing.risks")
> dFull <- d[event!=0] ## remove censoring
> dSurv <- d[event!=2] ## remove competing risk
>
> ## * no censoring
> test_that("wglm - no censoring",{
+ test <- wglm(regressor.event = ~ X1 + X8, formula.censor = Surv(time,event==0) ~ 1,
+ times = tau, data = dFull)
+
+ GS <- suppressWarnings(logitIPCW(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull))
+
+ expect_equal(coef(test, time = tau[5]), summary(GS)$coef[,"Estimate"], tol = 1e-5)
+ expect_equal(summary(test, print = FALSE)[[5]][,"Std. Error"], summary(GS)$coef[,"Std.Err"], tol = 1e-5)
+
+ ## ate
+ test.ate <- ate(test, data = dFull, times = tau, treatment = "X1", verbose = FALSE)
+ GS.ate <- logitATE(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull, treat.model = X1~1)
+ expect_equal(test.ate$diffRisk[5,estimate], GS.ate$difriskG, tol = 1e-5)
+ expect_equal(test.ate$diffRisk[5,se], GS.ate$se.difriskG, tol = 1e-5)
+ })
── Failure (???): wglm - no censoring ──────────────────────────────────────────
test.ate$diffRisk[5, estimate] not equal to GS.ate$difriskG.
names for current but not for target
Error in reporter$stop_if_needed() : Test failed
Calls: test_that -> <Anonymous>
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2022.03.22
Check: tests
Result: ERROR
Running ‘test-AUC.R’ [9s/12s]
Running ‘test-BinomialRegression.R’ [11s/14s]
Running ‘test-BrierScore.R’ [11s/14s]
Running ‘test-CauseSpecificCoxRegression.R’ [11s/13s]
Running ‘test-FineGrayRegression.R’ [8s/12s]
Running ‘test-boxplotScore.R’ [9s/11s]
Running ‘test-iidCox.R’ [12s/14s]
Running ‘test-phreg.R’ [15s/17s]
Running ‘test-predictCox.R’ [26s/33s]
Running ‘test-predictCoxPL.R’ [10s/13s]
Running ‘test-predictRisk-TD.R’ [10s/13s]
Running ‘test-predictRisk.R’ [11s/12s]
Running ‘test-score-bootstrap.R’ [34s/43s]
Running ‘test-score.R’ [19s/19s]
Running ‘test-summary-score.R’ [19s/22s]
Running ‘test-wglm.R’ [10s/12s]
Running the tests in ‘tests/test-wglm.R’ failed.
Complete output:
> ### test-wglm.R ---
> ##----------------------------------------------------------------------
> ## Author: Brice Ozenne
> ## Created: Dec 21 2021 (11:04)
> ## Version:
> ## Last-Updated: Dec 21 2021 (16:46)
> ## By: Brice Ozenne
> ## Update #: 16
> ##----------------------------------------------------------------------
> ##
> ### Commentary:
> ##
> ### Change Log:
> ##----------------------------------------------------------------------
> ##
> ### Code:
>
> ## * Packages
> library(testthat)
> library(data.table)
> library(mets)
Loading required package: timereg
Loading required package: survival
Loading required package: lava
Attaching package: 'lava'
The following object is masked from 'package:testthat':
compare
mets version 1.3.0
> library(riskRegression)
riskRegression version 2022.03.22
> library(survival)
>
> ## * Simulate data
> set.seed(10)
> n <- 250
> tau <- 1:5
> d <- sampleData(n, outcome = "competing.risks")
> dFull <- d[event!=0] ## remove censoring
> dSurv <- d[event!=2] ## remove competing risk
>
> ## * no censoring
> test_that("wglm - no censoring",{
+ test <- wglm(regressor.event = ~ X1 + X8, formula.censor = Surv(time,event==0) ~ 1,
+ times = tau, data = dFull)
+
+ GS <- suppressWarnings(logitIPCW(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull))
+
+ expect_equal(coef(test, time = tau[5]), summary(GS)$coef[,"Estimate"], tol = 1e-5)
+ expect_equal(summary(test, print = FALSE)[[5]][,"Std. Error"], summary(GS)$coef[,"Std.Err"], tol = 1e-5)
+
+ ## ate
+ test.ate <- ate(test, data = dFull, times = tau, treatment = "X1", verbose = FALSE)
+ GS.ate <- logitATE(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull, treat.model = X1~1)
+ expect_equal(test.ate$diffRisk[5,estimate], GS.ate$difriskG, tol = 1e-5)
+ expect_equal(test.ate$diffRisk[5,se], GS.ate$se.difriskG, tol = 1e-5)
+ })
── Failure (???): wglm - no censoring ──────────────────────────────────────────
test.ate$diffRisk[5, estimate] not equal to GS.ate$difriskG.
names for current but not for target
Error in reporter$stop_if_needed() : Test failed
Calls: test_that -> <Anonymous>
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2022.03.22
Check: tests
Result: ERROR
Running ‘test-AUC.R’ [9s/12s]
Running ‘test-BinomialRegression.R’ [12s/13s]
Running ‘test-BrierScore.R’ [11s/12s]
Running ‘test-CauseSpecificCoxRegression.R’ [12s/15s]
Running ‘test-FineGrayRegression.R’ [9s/10s]
Running ‘test-boxplotScore.R’ [9s/11s]
Running ‘test-iidCox.R’ [12s/15s]
Running ‘test-phreg.R’ [15s/17s]
Running ‘test-predictCox.R’ [27s/29s]
Running ‘test-predictCoxPL.R’ [11s/24s]
Running ‘test-predictRisk-TD.R’ [12s/23s]
Running ‘test-predictRisk.R’ [11s/24s]
Running ‘test-score-bootstrap.R’ [36s/62s]
Running ‘test-score.R’ [17s/20s]
Running ‘test-summary-score.R’ [18s/28s]
Running ‘test-wglm.R’ [10s/18s]
Running the tests in ‘tests/test-wglm.R’ failed.
Complete output:
> ### test-wglm.R ---
> ##----------------------------------------------------------------------
> ## Author: Brice Ozenne
> ## Created: Dec 21 2021 (11:04)
> ## Version:
> ## Last-Updated: Dec 21 2021 (16:46)
> ## By: Brice Ozenne
> ## Update #: 16
> ##----------------------------------------------------------------------
> ##
> ### Commentary:
> ##
> ### Change Log:
> ##----------------------------------------------------------------------
> ##
> ### Code:
>
> ## * Packages
> library(testthat)
> library(data.table)
> library(mets)
Loading required package: timereg
Loading required package: survival
Loading required package: lava
Attaching package: 'lava'
The following object is masked from 'package:testthat':
compare
mets version 1.3.0
> library(riskRegression)
riskRegression version 2022.03.22
> library(survival)
>
> ## * Simulate data
> set.seed(10)
> n <- 250
> tau <- 1:5
> d <- sampleData(n, outcome = "competing.risks")
> dFull <- d[event!=0] ## remove censoring
> dSurv <- d[event!=2] ## remove competing risk
>
> ## * no censoring
> test_that("wglm - no censoring",{
+ test <- wglm(regressor.event = ~ X1 + X8, formula.censor = Surv(time,event==0) ~ 1,
+ times = tau, data = dFull)
+
+ GS <- suppressWarnings(logitIPCW(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull))
+
+ expect_equal(coef(test, time = tau[5]), summary(GS)$coef[,"Estimate"], tol = 1e-5)
+ expect_equal(summary(test, print = FALSE)[[5]][,"Std. Error"], summary(GS)$coef[,"Std.Err"], tol = 1e-5)
+
+ ## ate
+ test.ate <- ate(test, data = dFull, times = tau, treatment = "X1", verbose = FALSE)
+ GS.ate <- logitATE(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull, treat.model = X1~1)
+ expect_equal(test.ate$diffRisk[5,estimate], GS.ate$difriskG, tol = 1e-5)
+ expect_equal(test.ate$diffRisk[5,se], GS.ate$se.difriskG, tol = 1e-5)
+ })
── Failure (???): wglm - no censoring ──────────────────────────────────────────
test.ate$diffRisk[5, estimate] not equal to GS.ate$difriskG.
names for current but not for target
Error in reporter$stop_if_needed() : Test failed
Calls: test_that -> <Anonymous>
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2022.03.22
Check: tests
Result: ERROR
Running 'test-AUC.R' [8s]
Running 'test-BinomialRegression.R' [9s]
Running 'test-BrierScore.R' [7s]
Running 'test-CauseSpecificCoxRegression.R' [9s]
Running 'test-FineGrayRegression.R' [6s]
Running 'test-boxplotScore.R' [6s]
Running 'test-iidCox.R' [11s]
Running 'test-phreg.R' [14s]
Running 'test-predictCox.R' [22s]
Running 'test-predictCoxPL.R' [9s]
Running 'test-predictRisk-TD.R' [9s]
Running 'test-predictRisk.R' [9s]
Running 'test-score-bootstrap.R' [29s]
Running 'test-score.R' [16s]
Running 'test-summary-score.R' [19s]
Running 'test-wglm.R' [9s]
Running the tests in 'tests/test-wglm.R' failed.
Complete output:
> ### test-wglm.R ---
> ##----------------------------------------------------------------------
> ## Author: Brice Ozenne
> ## Created: Dec 21 2021 (11:04)
> ## Version:
> ## Last-Updated: Dec 21 2021 (16:46)
> ## By: Brice Ozenne
> ## Update #: 16
> ##----------------------------------------------------------------------
> ##
> ### Commentary:
> ##
> ### Change Log:
> ##----------------------------------------------------------------------
> ##
> ### Code:
>
> ## * Packages
> library(testthat)
> library(data.table)
> library(mets)
Loading required package: timereg
Loading required package: survival
Loading required package: lava
Attaching package: 'lava'
The following object is masked from 'package:testthat':
compare
mets version 1.3.0
> library(riskRegression)
riskRegression version 2022.03.22
> library(survival)
>
> ## * Simulate data
> set.seed(10)
> n <- 250
> tau <- 1:5
> d <- sampleData(n, outcome = "competing.risks")
> dFull <- d[event!=0] ## remove censoring
> dSurv <- d[event!=2] ## remove competing risk
>
> ## * no censoring
> test_that("wglm - no censoring",{
+ test <- wglm(regressor.event = ~ X1 + X8, formula.censor = Surv(time,event==0) ~ 1,
+ times = tau, data = dFull)
+
+ GS <- suppressWarnings(logitIPCW(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull))
+
+ expect_equal(coef(test, time = tau[5]), summary(GS)$coef[,"Estimate"], tol = 1e-5)
+ expect_equal(summary(test, print = FALSE)[[5]][,"Std. Error"], summary(GS)$coef[,"Std.Err"], tol = 1e-5)
+
+ ## ate
+ test.ate <- ate(test, data = dFull, times = tau, treatment = "X1", verbose = FALSE)
+ GS.ate <- logitATE(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull, treat.model = X1~1)
+ expect_equal(test.ate$diffRisk[5,estimate], GS.ate$difriskG, tol = 1e-5)
+ expect_equal(test.ate$diffRisk[5,se], GS.ate$se.difriskG, tol = 1e-5)
+ })
── Failure (???): wglm - no censoring ──────────────────────────────────────────
test.ate$diffRisk[5, estimate] not equal to GS.ate$difriskG.
names for current but not for target
Error in reporter$stop_if_needed() : Test failed
Calls: test_that -> <Anonymous>
Execution halted
Flavor: r-devel-windows-x86_64
Version: 2022.03.22
Check: tests
Result: ERROR
Running ‘test-AUC.R’ [7s/8s]
Running ‘test-BinomialRegression.R’ [9s/10s]
Running ‘test-BrierScore.R’ [8s/9s]
Running ‘test-CauseSpecificCoxRegression.R’ [9s/11s]
Running ‘test-FineGrayRegression.R’ [6s/7s]
Running ‘test-boxplotScore.R’ [7s/7s]
Running ‘test-iidCox.R’ [10s/11s]
Running ‘test-phreg.R’ [13s/14s]
Running ‘test-predictCox.R’ [21s/25s]
Running ‘test-predictCoxPL.R’ [8s/11s]
Running ‘test-predictRisk-TD.R’ [9s/11s]
Running ‘test-predictRisk.R’ [8s/10s]
Running ‘test-score-bootstrap.R’ [27s/31s]
Running ‘test-score.R’ [14s/17s]
Running ‘test-summary-score.R’ [13s/15s]
Running ‘test-wglm.R’ [8s/9s]
Running the tests in ‘tests/test-wglm.R’ failed.
Complete output:
> ### test-wglm.R ---
> ##----------------------------------------------------------------------
> ## Author: Brice Ozenne
> ## Created: Dec 21 2021 (11:04)
> ## Version:
> ## Last-Updated: Dec 21 2021 (16:46)
> ## By: Brice Ozenne
> ## Update #: 16
> ##----------------------------------------------------------------------
> ##
> ### Commentary:
> ##
> ### Change Log:
> ##----------------------------------------------------------------------
> ##
> ### Code:
>
> ## * Packages
> library(testthat)
> library(data.table)
> library(mets)
Loading required package: timereg
Loading required package: survival
Loading required package: lava
Attaching package: 'lava'
The following object is masked from 'package:testthat':
compare
mets version 1.3.0
> library(riskRegression)
riskRegression version 2022.03.22
> library(survival)
>
> ## * Simulate data
> set.seed(10)
> n <- 250
> tau <- 1:5
> d <- sampleData(n, outcome = "competing.risks")
> dFull <- d[event!=0] ## remove censoring
> dSurv <- d[event!=2] ## remove competing risk
>
> ## * no censoring
> test_that("wglm - no censoring",{
+ test <- wglm(regressor.event = ~ X1 + X8, formula.censor = Surv(time,event==0) ~ 1,
+ times = tau, data = dFull)
+
+ GS <- suppressWarnings(logitIPCW(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull))
+
+ expect_equal(coef(test, time = tau[5]), summary(GS)$coef[,"Estimate"], tol = 1e-5)
+ expect_equal(summary(test, print = FALSE)[[5]][,"Std. Error"], summary(GS)$coef[,"Std.Err"], tol = 1e-5)
+
+ ## ate
+ test.ate <- ate(test, data = dFull, times = tau, treatment = "X1", verbose = FALSE)
+ GS.ate <- logitATE(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull, treat.model = X1~1)
+ expect_equal(test.ate$diffRisk[5,estimate], GS.ate$difriskG, tol = 1e-5)
+ expect_equal(test.ate$diffRisk[5,se], GS.ate$se.difriskG, tol = 1e-5)
+ })
── Failure (???): wglm - no censoring ──────────────────────────────────────────
test.ate$diffRisk[5, estimate] not equal to GS.ate$difriskG.
names for current but not for target
Error in reporter$stop_if_needed() : Test failed
Calls: test_that -> <Anonymous>
Execution halted
Flavor: r-patched-linux-x86_64
Version: 2022.03.22
Check: tests
Result: ERROR
Running ‘test-AUC.R’ [7s/9s]
Running ‘test-BinomialRegression.R’ [9s/10s]
Running ‘test-BrierScore.R’ [9s/10s]
Running ‘test-CauseSpecificCoxRegression.R’ [9s/10s]
Running ‘test-FineGrayRegression.R’ [7s/7s]
Running ‘test-boxplotScore.R’ [7s/7s]
Running ‘test-iidCox.R’ [10s/11s]
Running ‘test-phreg.R’ [12s/14s]
Running ‘test-predictCox.R’ [21s/25s]
Running ‘test-predictCoxPL.R’ [8s/9s]
Running ‘test-predictRisk-TD.R’ [9s/10s]
Running ‘test-predictRisk.R’ [8s/11s]
Running ‘test-score-bootstrap.R’ [27s/31s]
Running ‘test-score.R’ [14s/17s]
Running ‘test-summary-score.R’ [13s/14s]
Running ‘test-wglm.R’ [8s/9s]
Running the tests in ‘tests/test-wglm.R’ failed.
Complete output:
> ### test-wglm.R ---
> ##----------------------------------------------------------------------
> ## Author: Brice Ozenne
> ## Created: Dec 21 2021 (11:04)
> ## Version:
> ## Last-Updated: Dec 21 2021 (16:46)
> ## By: Brice Ozenne
> ## Update #: 16
> ##----------------------------------------------------------------------
> ##
> ### Commentary:
> ##
> ### Change Log:
> ##----------------------------------------------------------------------
> ##
> ### Code:
>
> ## * Packages
> library(testthat)
> library(data.table)
> library(mets)
Loading required package: timereg
Loading required package: survival
Loading required package: lava
Attaching package: 'lava'
The following object is masked from 'package:testthat':
compare
mets version 1.3.0
> library(riskRegression)
riskRegression version 2022.03.22
> library(survival)
>
> ## * Simulate data
> set.seed(10)
> n <- 250
> tau <- 1:5
> d <- sampleData(n, outcome = "competing.risks")
> dFull <- d[event!=0] ## remove censoring
> dSurv <- d[event!=2] ## remove competing risk
>
> ## * no censoring
> test_that("wglm - no censoring",{
+ test <- wglm(regressor.event = ~ X1 + X8, formula.censor = Surv(time,event==0) ~ 1,
+ times = tau, data = dFull)
+
+ GS <- suppressWarnings(logitIPCW(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull))
+
+ expect_equal(coef(test, time = tau[5]), summary(GS)$coef[,"Estimate"], tol = 1e-5)
+ expect_equal(summary(test, print = FALSE)[[5]][,"Std. Error"], summary(GS)$coef[,"Std.Err"], tol = 1e-5)
+
+ ## ate
+ test.ate <- ate(test, data = dFull, times = tau, treatment = "X1", verbose = FALSE)
+ GS.ate <- logitATE(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull, treat.model = X1~1)
+ expect_equal(test.ate$diffRisk[5,estimate], GS.ate$difriskG, tol = 1e-5)
+ expect_equal(test.ate$diffRisk[5,se], GS.ate$se.difriskG, tol = 1e-5)
+ })
── Failure (???): wglm - no censoring ──────────────────────────────────────────
test.ate$diffRisk[5, estimate] not equal to GS.ate$difriskG.
names for current but not for target
Error in reporter$stop_if_needed() : Test failed
Calls: test_that -> <Anonymous>
Execution halted
Flavor: r-release-linux-x86_64
Version: 2022.03.22
Check: installed package size
Result: NOTE
installed size is 10.8Mb
sub-directories of 1Mb or more:
libs 9.3Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 2022.03.22
Check: tests
Result: ERROR
Running 'test-AUC.R' [8s]
Running 'test-BinomialRegression.R' [10s]
Running 'test-BrierScore.R' [9s]
Running 'test-CauseSpecificCoxRegression.R' [9s]
Running 'test-FineGrayRegression.R' [7s]
Running 'test-boxplotScore.R' [8s]
Running 'test-iidCox.R' [11s]
Running 'test-phreg.R' [13s]
Running 'test-predictCox.R' [25s]
Running 'test-predictCoxPL.R' [9s]
Running 'test-predictRisk-TD.R' [10s]
Running 'test-predictRisk.R' [9s]
Running 'test-score-bootstrap.R' [30s]
Running 'test-score.R' [15s]
Running 'test-summary-score.R' [16s]
Running 'test-wglm.R' [9s]
Running the tests in 'tests/test-wglm.R' failed.
Complete output:
> ### test-wglm.R ---
> ##----------------------------------------------------------------------
> ## Author: Brice Ozenne
> ## Created: Dec 21 2021 (11:04)
> ## Version:
> ## Last-Updated: Dec 21 2021 (16:46)
> ## By: Brice Ozenne
> ## Update #: 16
> ##----------------------------------------------------------------------
> ##
> ### Commentary:
> ##
> ### Change Log:
> ##----------------------------------------------------------------------
> ##
> ### Code:
>
> ## * Packages
> library(testthat)
> library(data.table)
> library(mets)
Loading required package: timereg
Loading required package: survival
Loading required package: lava
Attaching package: 'lava'
The following object is masked from 'package:testthat':
compare
mets version 1.3.0
> library(riskRegression)
riskRegression version 2022.03.22
> library(survival)
>
> ## * Simulate data
> set.seed(10)
> n <- 250
> tau <- 1:5
> d <- sampleData(n, outcome = "competing.risks")
> dFull <- d[event!=0] ## remove censoring
> dSurv <- d[event!=2] ## remove competing risk
>
> ## * no censoring
> test_that("wglm - no censoring",{
+ test <- wglm(regressor.event = ~ X1 + X8, formula.censor = Surv(time,event==0) ~ 1,
+ times = tau, data = dFull)
+
+ GS <- suppressWarnings(logitIPCW(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull))
+
+ expect_equal(coef(test, time = tau[5]), summary(GS)$coef[,"Estimate"], tol = 1e-5)
+ expect_equal(summary(test, print = FALSE)[[5]][,"Std. Error"], summary(GS)$coef[,"Std.Err"], tol = 1e-5)
+
+ ## ate
+ test.ate <- ate(test, data = dFull, times = tau, treatment = "X1", verbose = FALSE)
+ GS.ate <- logitATE(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull, treat.model = X1~1)
+ expect_equal(test.ate$diffRisk[5,estimate], GS.ate$difriskG, tol = 1e-5)
+ expect_equal(test.ate$diffRisk[5,se], GS.ate$se.difriskG, tol = 1e-5)
+ })
── Failure (???): wglm - no censoring ──────────────────────────────────────────
test.ate$diffRisk[5, estimate] not equal to GS.ate$difriskG.
names for current but not for target
Error in reporter$stop_if_needed() : Test failed
Calls: test_that -> <Anonymous>
Execution halted
Flavor: r-release-windows-x86_64
Version: 2022.03.22
Check: running tests for arch ‘i386’
Result: ERROR
Running 'test-AUC.R' [8s]
Running 'test-BinomialRegression.R' [9s]
Running 'test-BrierScore.R' [9s]
Running 'test-CauseSpecificCoxRegression.R' [9s]
Running 'test-FineGrayRegression.R' [7s]
Running 'test-boxplotScore.R' [7s]
Running 'test-iidCox.R' [11s]
Running 'test-phreg.R' [12s]
Running 'test-predictCox.R' [24s]
Running 'test-predictCoxPL.R' [9s]
Running 'test-predictRisk-TD.R' [10s]
Running 'test-predictRisk.R' [10s]
Running 'test-score-bootstrap.R' [30s]
Running 'test-score.R' [15s]
Running 'test-summary-score.R' [15s]
Running 'test-wglm.R' [8s]
Running the tests in 'tests/test-wglm.R' failed.
Complete output:
> ### test-wglm.R ---
> ##----------------------------------------------------------------------
> ## Author: Brice Ozenne
> ## Created: Dec 21 2021 (11:04)
> ## Version:
> ## Last-Updated: Dec 21 2021 (16:46)
> ## By: Brice Ozenne
> ## Update #: 16
> ##----------------------------------------------------------------------
> ##
> ### Commentary:
> ##
> ### Change Log:
> ##----------------------------------------------------------------------
> ##
> ### Code:
>
> ## * Packages
> library(testthat)
> library(data.table)
> library(mets)
Loading required package: timereg
Loading required package: survival
Loading required package: lava
Attaching package: 'lava'
The following object is masked from 'package:testthat':
compare
mets version 1.3.0
> library(riskRegression)
riskRegression version 2022.03.22
> library(survival)
>
> ## * Simulate data
> set.seed(10)
> n <- 250
> tau <- 1:5
> d <- sampleData(n, outcome = "competing.risks")
> dFull <- d[event!=0] ## remove censoring
> dSurv <- d[event!=2] ## remove competing risk
>
> ## * no censoring
> test_that("wglm - no censoring",{
+ test <- wglm(regressor.event = ~ X1 + X8, formula.censor = Surv(time,event==0) ~ 1,
+ times = tau, data = dFull)
+
+ GS <- suppressWarnings(logitIPCW(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull))
+
+ expect_equal(coef(test, time = tau[5]), summary(GS)$coef[,"Estimate"], tol = 1e-5)
+ expect_equal(summary(test, print = FALSE)[[5]][,"Std. Error"], summary(GS)$coef[,"Std.Err"], tol = 1e-5)
+
+ ## ate
+ test.ate <- ate(test, data = dFull, times = tau, treatment = "X1", verbose = FALSE)
+ GS.ate <- logitATE(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull, treat.model = X1~1)
+ expect_equal(test.ate$diffRisk[5,estimate], GS.ate$difriskG, tol = 1e-5)
+ expect_equal(test.ate$diffRisk[5,se], GS.ate$se.difriskG, tol = 1e-5)
+ })
-- Failure (???): wglm - no censoring ------------------------------------------
test.ate$diffRisk[5, estimate] not equal to GS.ate$difriskG.
names for current but not for target
Error in reporter$stop_if_needed() : Test failed
Calls: test_that -> <Anonymous>
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64
Version: 2022.03.22
Check: running tests for arch ‘x64’
Result: ERROR
Running 'test-AUC.R' [8s]
Running 'test-BinomialRegression.R' [10s]
Running 'test-BrierScore.R' [9s]
Running 'test-CauseSpecificCoxRegression.R' [9s]
Running 'test-FineGrayRegression.R' [7s]
Running 'test-boxplotScore.R' [7s]
Running 'test-iidCox.R' [12s]
Running 'test-phreg.R' [13s]
Running 'test-predictCox.R' [24s]
Running 'test-predictCoxPL.R' [10s]
Running 'test-predictRisk-TD.R' [10s]
Running 'test-predictRisk.R' [9s]
Running 'test-score-bootstrap.R' [31s]
Running 'test-score.R' [15s]
Running 'test-summary-score.R' [14s]
Running 'test-wglm.R' [8s]
Running the tests in 'tests/test-wglm.R' failed.
Complete output:
> ### test-wglm.R ---
> ##----------------------------------------------------------------------
> ## Author: Brice Ozenne
> ## Created: Dec 21 2021 (11:04)
> ## Version:
> ## Last-Updated: Dec 21 2021 (16:46)
> ## By: Brice Ozenne
> ## Update #: 16
> ##----------------------------------------------------------------------
> ##
> ### Commentary:
> ##
> ### Change Log:
> ##----------------------------------------------------------------------
> ##
> ### Code:
>
> ## * Packages
> library(testthat)
> library(data.table)
> library(mets)
Loading required package: timereg
Loading required package: survival
Loading required package: lava
Attaching package: 'lava'
The following object is masked from 'package:testthat':
compare
mets version 1.3.0
> library(riskRegression)
riskRegression version 2022.03.22
> library(survival)
>
> ## * Simulate data
> set.seed(10)
> n <- 250
> tau <- 1:5
> d <- sampleData(n, outcome = "competing.risks")
> dFull <- d[event!=0] ## remove censoring
> dSurv <- d[event!=2] ## remove competing risk
>
> ## * no censoring
> test_that("wglm - no censoring",{
+ test <- wglm(regressor.event = ~ X1 + X8, formula.censor = Surv(time,event==0) ~ 1,
+ times = tau, data = dFull)
+
+ GS <- suppressWarnings(logitIPCW(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull))
+
+ expect_equal(coef(test, time = tau[5]), summary(GS)$coef[,"Estimate"], tol = 1e-5)
+ expect_equal(summary(test, print = FALSE)[[5]][,"Std. Error"], summary(GS)$coef[,"Std.Err"], tol = 1e-5)
+
+ ## ate
+ test.ate <- ate(test, data = dFull, times = tau, treatment = "X1", verbose = FALSE)
+ GS.ate <- logitATE(formula = Event(time,event)~X1 + X8,
+ time = tau[5], data = dFull, treat.model = X1~1)
+ expect_equal(test.ate$diffRisk[5,estimate], GS.ate$difriskG, tol = 1e-5)
+ expect_equal(test.ate$diffRisk[5,se], GS.ate$se.difriskG, tol = 1e-5)
+ })
-- Failure (???): wglm - no censoring ------------------------------------------
test.ate$diffRisk[5, estimate] not equal to GS.ate$difriskG.
names for current but not for target
Error in reporter$stop_if_needed() : Test failed
Calls: test_that -> <Anonymous>
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64