Last updated on 2026-08-01 17:50:29 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.1 | 8.56 | 86.78 | 95.34 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.1 | 6.65 | 65.96 | 72.61 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.1 | 15.00 | 132.22 | 147.22 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.1 | 67.57 | ERROR | |||
| r-devel-windows-x86_64 | 0.1.1 | 11.00 | 91.00 | 102.00 | ERROR | |
| r-patched-linux-x86_64 | 0.1.1 | 8.85 | 80.49 | 89.34 | ERROR | |
| r-release-linux-x86_64 | 0.1.1 | 7.91 | 78.98 | 86.89 | ERROR | |
| r-release-macos-arm64 | 0.1.1 | 2.00 | 34.00 | 36.00 | OK | |
| r-release-macos-x86_64 | 0.1.1 | 6.00 | 139.00 | 145.00 | OK | |
| r-release-windows-x86_64 | 0.1.1 | 11.00 | 92.00 | 103.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.1.1 | OK | ||||
| r-oldrel-macos-x86_64 | 0.1.1 | 6.00 | 129.00 | 135.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.1 | 14.00 | 115.00 | 129.00 | ERROR |
Version: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(jointCompRisk)
>
> test_check("jointCompRisk")
Saving _problems/test-basic-32.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-basic.R:32:3'): do_cif_analysis returns formatted summaries ────
Error in `survfit.formula(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)`: the etype argument is no longer supported, use a factor as the status variable
Backtrace:
▆
1. └─jointCompRisk::do_cif_analysis(prepped, tau = 15) at test-basic.R:32:3
2. └─jointCompRisk:::table1_cif(Treatment, Control, tau, 0, 1, 0)
3. └─jointCompRisk:::auc.var.joint(data1, tau, a, b, c)
4. ├─survival::survfit(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)
5. └─survival::survfit.formula(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘Example_analysis.Rmd’ using rmarkdown
Quitting from Example_analysis.Rmd:24-42 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `survfit.formula()`:
! the etype argument is no longer supported, use a factor as the status variable
---
Backtrace:
▆
1. └─jointCompRisk::do_cif_analysis(mydata_std, tau = 15)
2. └─jointCompRisk:::table1_cif(Treatment, Control, tau, 0, 1, 0)
3. └─jointCompRisk:::auc.var.joint(data1, tau, a, b, c)
4. ├─survival::survfit(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)
5. └─survival::survfit.formula(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Example_analysis.Rmd' failed with diagnostics:
the etype argument is no longer supported, use a factor as the status variable
--- failed re-building ‘Example_analysis.Rmd’
--- re-building ‘Vignette.Rmd’ using rmarkdown
main_df package:jointCompRisk R Documentation
_<08>M_<08>a_<08>i_<08>n _<08>C_<08>o_<08>m_<08>p_<08>e_<08>t_<08>i_<08>n_<08>g _<08>R_<08>i_<08>s_<08>k_<08>s _<08>D_<08>a_<08>t_<08>a_<08>s_<08>e_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>e_<08>d _<08>c_<08>l_<08>i_<08>n_<08>i_<08>c_<08>a_<08>l _<08>t_<08>r_<08>i_<08>a_<08>l _<08>d_<08>a_<08>t_<08>a _<08>w_<08>i_<08>t_<08>h
_<08>c_<08>o_<08>m_<08>p_<08>e_<08>t_<08>i_<08>n_<08>g _<08>r_<08>i_<08>s_<08>k_<08>s _<08>s_<08>u_<08>r_<08>v_<08>i_<08>v_<08>a_<08>l _<08>o_<08>u_<08>t_<08>c_<08>o_<08>m_<08>e_<08>s. _<08>T_<08>h_<08>i_<08>s _<08>d_<08>a_<08>t_<08>a_<08>s_<08>e_<08>t _<08>f_<08>o_<08>l_<08>l_<08>o_<08>w_<08>s _<08>t_<08>h_<08>e _<08>s_<08>t_<08>r_<08>u_<08>c_<08>t_<08>u_<08>r_<08>e
_<08>o_<08>f _<08>A_<08>d_<08>a_<08>p_<08>t_<08>i_<08>v_<08>e _<08>C_<08>O_<08>V_<08>I_<08>D-_<08>1_<08>9 _<08>T_<08>r_<08>e_<08>a_<08>t_<08>m_<08>e_<08>n_<08>t _<08>T_<08>r_<08>i_<08>a_<08>l_<08>s (_<08>A_<08>C_<08>T_<08>T) _<08>w_<08>i_<08>t_<08>h _<08>b_<08>u_<08>i_<08>l_<08>t-_<08>i_<08>n _<08>t_<08>r_<08>e_<08>a_<08>t_<08>m_<08>e_<08>n_<08>t
_<08>e_<08>f_<08>f_<08>e_<08>c_<08>t_<08>s _<08>f_<08>o_<08>r _<08>d_<08>e_<08>m_<08>o_<08>n_<08>s_<08>t_<08>r_<08>a_<08>t_<08>i_<08>o_<08>n _<08>p_<08>u_<08>r_<08>p_<08>o_<08>s_<08>e_<08>s.
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Main Competing Risks Dataset Simulated clinical trial data with
competing risks survival outcomes. This dataset follows the
structure of Adaptive COVID-19 Treatment Trials (ACTT) with
built-in treatment effects for demonstration purposes.
_<08>U_<08>s_<08>a_<08>g_<08>e:
data(main_df)
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
A data frame with 150 rows and 7 variables:
ID
Patient identifier (character)
TimeToRecovery
Time to recovery event in days (numeric)
TimeToDeath
Time to death event in days (numeric)
RecoveryCensoringIndicator
Recovery censoring indicator (0=event observed, 1=censored)
DeathCensoringIndicator
Death censoring indicator (0=event observed, 1=censored)
BaselineScore
Baseline severity score, range 4-7 (numeric)
Treatment
Treatment arm indicator (0=control, 1=treatment)
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
This is a simulated dataset created for demonstration purposes
with realistic treatment effects built in: treatment group has
1.5× faster recovery times and 1.8× improved survival compared to
control. The data represents a clinical trial with competing risks
where patients can either recover or die, with administrative
censoring at 30 days.
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
Simulated data based on Weibull distributions with
treatment-specific parameters
_<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
data(main_df)
head(main_df)
summary(main_df)
# Compare outcomes by treatment
tapply(main_df$TimeToRecovery, main_df$Treatment, summary)
tapply(main_df$TimeToDeath, main_df$Treatment, summary)
long_df package:jointCompRisk R Documentation
_<08>L_<08>o_<08>n_<08>g_<08>i_<08>t_<08>u_<08>d_<08>i_<08>n_<08>a_<08>l _<08>S_<08>e_<08>v_<08>e_<08>r_<08>i_<08>t_<08>y _<08>S_<08>c_<08>o_<08>r_<08>e_<08>s _<08>D_<08>a_<08>t_<08>a_<08>s_<08>e_<08>t
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Repeated measurements of ordinal severity scores over time for the
same patients in the main_df dataset, with treatment-specific
trajectory patterns.
_<08>U_<08>s_<08>a_<08>g_<08>e:
data(long_df)
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
A data frame with variable rows per patient:
PersonID
Patient identifier matching ID in main_df (character)
OrdinalScore
Severity score on 1-8 scale (numeric)
RelativeDay
Study day (numeric) starting from day 0 (baseline)
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
Measurements are taken at scheduled visits: days 0 (baseline), 1,
3, 5, 7, 10, 14, 18, 21, 25, 28. The trajectory follows
treatment-specific probabilities: treatment patients have 45 and
15 worsening probability, creating realistic differential clinical
progression patterns.
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
Simulated data using treatment-specific random walk with
boundaries
_<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
data(long_df)
data(main_df)
head(long_df)
# See data for first patient
subset(long_df, PersonID == "Patient_001")
# Compare average scores by treatment
long_df %>%
dplyr::left_join(main_df[,c("ID","Treatment")], by=c("PersonID"="ID")) %>%
dplyr::group_by(Treatment) %>%
dplyr::summarise(mean_score = mean(OrdinalScore))
Quitting from Vignette.Rmd:159-169 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `survfit.formula()`:
! the etype argument is no longer supported, use a factor as the status variable
---
Backtrace:
▆
1. └─jointCompRisk::do_cif_analysis(mydata_std, tau = 15)
2. └─jointCompRisk:::table1_cif(Treatment, Control, tau, 0, 1, 0)
3. └─jointCompRisk:::auc.var.joint(data1, tau, a, b, c)
4. ├─survival::survfit(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)
5. └─survival::survfit.formula(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
the etype argument is no longer supported, use a factor as the status variable
--- failed re-building ‘Vignette.Rmd’
SUMMARY: processing the following files failed:
‘Example_analysis.Rmd’ ‘Vignette.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: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(jointCompRisk)
>
> test_check("jointCompRisk")
Saving _problems/test-basic-32.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-basic.R:32:3'): do_cif_analysis returns formatted summaries ────
Error in `survfit.formula(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)`: the etype argument is no longer supported, use a factor as the status variable
Backtrace:
▆
1. └─jointCompRisk::do_cif_analysis(prepped, tau = 15) at test-basic.R:32:3
2. └─jointCompRisk:::table1_cif(Treatment, Control, tau, 0, 1, 0)
3. └─jointCompRisk:::auc.var.joint(data1, tau, a, b, c)
4. ├─survival::survfit(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)
5. └─survival::survfit.formula(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.1
Check: for new files in some other directories
Result: NOTE
Found the following files/directories:
‘~/tmp/scratch/Rtmp011pmc’ ‘~/tmp/scratch/Rtmp096JLV’
‘~/tmp/scratch/Rtmp0XOfKi’ ‘~/tmp/scratch/Rtmp12X8iY’
‘~/tmp/scratch/Rtmp13w4FS’ ‘~/tmp/scratch/Rtmp141FuF’
‘~/tmp/scratch/Rtmp19OG2S’ ‘~/tmp/scratch/Rtmp1Mj4JO’
‘~/tmp/scratch/Rtmp2T62Ze’ ‘~/tmp/scratch/Rtmp3PCC5l’
‘~/tmp/scratch/Rtmp47lCeY’ ‘~/tmp/scratch/Rtmp4YqnyN’
‘~/tmp/scratch/Rtmp6ac2Kq’ ‘~/tmp/scratch/Rtmp6oficT’
‘~/tmp/scratch/Rtmp7NZnKx’ ‘~/tmp/scratch/Rtmp7qhuQz’
‘~/tmp/scratch/Rtmp8pCbYq’ ‘~/tmp/scratch/Rtmp942zcF’
‘~/tmp/scratch/Rtmp9EA1AE’ ‘~/tmp/scratch/Rtmp9wtSRr’
‘~/tmp/scratch/RtmpA3k2I0’ ‘~/tmp/scratch/RtmpBigVXr’
‘~/tmp/scratch/RtmpBpA7ju’ ‘~/tmp/scratch/RtmpBvmRIH’
‘~/tmp/scratch/RtmpCxDopq’ ‘~/tmp/scratch/RtmpDfjOpE’
‘~/tmp/scratch/RtmpDgJ8sW’ ‘~/tmp/scratch/RtmpEHfiEG’
‘~/tmp/scratch/RtmpENhzV7’ ‘~/tmp/scratch/RtmpEOGm2r’
‘~/tmp/scratch/RtmpES93HN’ ‘~/tmp/scratch/RtmpEmYyOX’
‘~/tmp/scratch/RtmpEpg7hz’ ‘~/tmp/scratch/RtmpFiJodj’
‘~/tmp/scratch/RtmpGee0lj’ ‘~/tmp/scratch/RtmpGnghKF’
‘~/tmp/scratch/RtmpGonGW4’ ‘~/tmp/scratch/RtmpIxvC90’
‘~/tmp/scratch/RtmpJgwdcY’ ‘~/tmp/scratch/RtmpJiv52i’
‘~/tmp/scratch/RtmpJtdN6u’ ‘~/tmp/scratch/RtmpKVkOpg’
‘~/tmp/scratch/RtmpKzgnjj’ ‘~/tmp/scratch/RtmpLKh4p3’
‘~/tmp/scratch/RtmpLpHe5V’ ‘~/tmp/scratch/RtmpLpa5A9’
‘~/tmp/scratch/RtmpNWm1WZ’ ‘~/tmp/scratch/RtmpO0jJa1’
‘~/tmp/scratch/RtmpO5cPWB’ ‘~/tmp/scratch/RtmpOReQDf’
‘~/tmp/scratch/RtmpOUWgnq’ ‘~/tmp/scratch/RtmpOeY8WF’
‘~/tmp/scratch/RtmpP38XR9’ ‘~/tmp/scratch/RtmpPkVXa9’
‘~/tmp/scratch/RtmpPwbRRY’ ‘~/tmp/scratch/RtmpRTRxFe’
‘~/tmp/scratch/RtmpRWNr8r’ ‘~/tmp/scratch/RtmpRoajU8’
‘~/tmp/scratch/RtmpRvSnoZ’ ‘~/tmp/scratch/RtmpS1rv3f’
‘~/tmp/scratch/RtmpS9vTca’ ‘~/tmp/scratch/RtmpSFUhxL’
‘~/tmp/scratch/RtmpSHRPjT’ ‘~/tmp/scratch/RtmpSaBtKf’
‘~/tmp/scratch/RtmpSp7e1o’ ‘~/tmp/scratch/RtmpSqzkZ4’
‘~/tmp/scratch/RtmpU2Pq1G’ ‘~/tmp/scratch/RtmpVIsmMh’
‘~/tmp/scratch/RtmpVfUEz5’ ‘~/tmp/scratch/RtmpVu7Yzw’
‘~/tmp/scratch/RtmpWZNwxi’ ‘~/tmp/scratch/RtmpXMHCzg’
‘~/tmp/scratch/RtmpXmVvkn’ ‘~/tmp/scratch/RtmpY37ta3’
‘~/tmp/scratch/RtmpZEYJPm’ ‘~/tmp/scratch/RtmpZPSbRf’
‘~/tmp/scratch/RtmpZuUUyB’ ‘~/tmp/scratch/RtmpZuenAW’
‘~/tmp/scratch/RtmpaHUES0’ ‘~/tmp/scratch/RtmpavzIFL’
‘~/tmp/scratch/RtmpbFETBj’ ‘~/tmp/scratch/RtmpdAIADu’
‘~/tmp/scratch/RtmpdlZjJy’ ‘~/tmp/scratch/RtmpegEzw9’
‘~/tmp/scratch/RtmpewWUow’ ‘~/tmp/scratch/Rtmpf2VFfN’
‘~/tmp/scratch/RtmpfG6PKp’ ‘~/tmp/scratch/RtmpfLl6Nm’
‘~/tmp/scratch/RtmpfSkPkF’ ‘~/tmp/scratch/RtmpgIgc5m’
‘~/tmp/scratch/RtmpgK19Aq’ ‘~/tmp/scratch/RtmpgkclVZ’
‘~/tmp/scratch/RtmphO6xhz’ ‘~/tmp/scratch/RtmpiOGQZH’
‘~/tmp/scratch/Rtmpiehnoj’ ‘~/tmp/scratch/Rtmpj9RuSy’
‘~/tmp/scratch/Rtmpk2UFvl’ ‘~/tmp/scratch/RtmpkTHYmA’
‘~/tmp/scratch/Rtmpkkyfwv’ ‘~/tmp/scratch/Rtmpko0SZ4’
‘~/tmp/scratch/Rtmpl4wSzh’ ‘~/tmp/scratch/RtmplT1Zoa’
‘~/tmp/scratch/Rtmplzmyd4’ ‘~/tmp/scratch/RtmpnV3o0T’
‘~/tmp/scratch/RtmpnwS0ej’ ‘~/tmp/scratch/RtmpoPf3Pq’
‘~/tmp/scratch/Rtmpp29bGm’ ‘~/tmp/scratch/RtmppHHh0a’
‘~/tmp/scratch/RtmppSfseY’ ‘~/tmp/scratch/RtmppVG0L6’
‘~/tmp/scratch/RtmppoONiR’ ‘~/tmp/scratch/Rtmpq5nokl’
‘~/tmp/scratch/RtmpqDg9gM’ ‘~/tmp/scratch/Rtmpqb7rMK’
‘~/tmp/scratch/Rtmpqcuis6’ ‘~/tmp/scratch/Rtmpqlmo8q’
‘~/tmp/scratch/RtmpsFeLuc’ ‘~/tmp/scratch/RtmpsLWjoK’
‘~/tmp/scratch/RtmpswqcZR’ ‘~/tmp/scratch/RtmptIWeso’
‘~/tmp/scratch/RtmptdXykZ’ ‘~/tmp/scratch/RtmptfvzsV’
‘~/tmp/scratch/Rtmpu79fK0’ ‘~/tmp/scratch/RtmpuUUbkk’
‘~/tmp/scratch/Rtmpuax4Rw’ ‘~/tmp/scratch/RtmpukKaRc’
‘~/tmp/scratch/RtmpuwPYlV’ ‘~/tmp/scratch/RtmpwJmBjH’
‘~/tmp/scratch/RtmpwmjIJG’ ‘~/tmp/scratch/RtmpwuEmch’
‘~/tmp/scratch/RtmpwyFrOK’ ‘~/tmp/scratch/RtmpxQTozG’
‘~/tmp/scratch/RtmpyGjqiW’ ‘~/tmp/scratch/RtmpyYGXrF’
‘~/tmp/scratch/Rtmpybg8Vh’ ‘~/tmp/scratch/RtmpzjGeB2’
‘~/tmp/scratch/Rtmpzl9SsI’ ‘~/tmp/scratch/RtmpzradxZ’
‘~/tmp/scratch/xvfb-run.0gWh9e’ ‘~/tmp/scratch/xvfb-run.12HRWt’
‘~/tmp/scratch/xvfb-run.17amJh’ ‘~/tmp/scratch/xvfb-run.1jyNGs’
‘~/tmp/scratch/xvfb-run.35hh6i’ ‘~/tmp/scratch/xvfb-run.3m5Ttq’
‘~/tmp/scratch/xvfb-run.45JwT3’ ‘~/tmp/scratch/xvfb-run.4YVhr0’
‘~/tmp/scratch/xvfb-run.9lcWyw’ ‘~/tmp/scratch/xvfb-run.AgDh06’
‘~/tmp/scratch/xvfb-run.CnjEUZ’ ‘~/tmp/scratch/xvfb-run.DMGwlF’
‘~/tmp/scratch/xvfb-run.EOiSc5’ ‘~/tmp/scratch/xvfb-run.GCIF8R’
‘~/tmp/scratch/xvfb-run.Gnf3cv’ ‘~/tmp/scratch/xvfb-run.HhOded’
‘~/tmp/scratch/xvfb-run.JC0Sm8’ ‘~/tmp/scratch/xvfb-run.KgVmiZ’
‘~/tmp/scratch/xvfb-run.LUcCfP’ ‘~/tmp/scratch/xvfb-run.LlgOon’
‘~/tmp/scratch/xvfb-run.NvhEmQ’ ‘~/tmp/scratch/xvfb-run.SOgbz4’
‘~/tmp/scratch/xvfb-run.TEB7Wu’ ‘~/tmp/scratch/xvfb-run.TOpr7c’
‘~/tmp/scratch/xvfb-run.TUqE0U’ ‘~/tmp/scratch/xvfb-run.TmLrxC’
‘~/tmp/scratch/xvfb-run.Tucq1Y’ ‘~/tmp/scratch/xvfb-run.VcZc7j’
‘~/tmp/scratch/xvfb-run.WcXrKl’ ‘~/tmp/scratch/xvfb-run.XtilFS’
‘~/tmp/scratch/xvfb-run.YK4XvB’ ‘~/tmp/scratch/xvfb-run.YQzi1t’
‘~/tmp/scratch/xvfb-run.YnIEgM’ ‘~/tmp/scratch/xvfb-run.a5sqsN’
‘~/tmp/scratch/xvfb-run.a7bf1y’ ‘~/tmp/scratch/xvfb-run.aMEXgv’
‘~/tmp/scratch/xvfb-run.aYZjMf’ ‘~/tmp/scratch/xvfb-run.b56rm1’
‘~/tmp/scratch/xvfb-run.bJ6M1V’ ‘~/tmp/scratch/xvfb-run.boyPkw’
‘~/tmp/scratch/xvfb-run.bp9GsU’ ‘~/tmp/scratch/xvfb-run.dPf6f8’
‘~/tmp/scratch/xvfb-run.eWJ0uE’ ‘~/tmp/scratch/xvfb-run.eZ8cnD’
‘~/tmp/scratch/xvfb-run.egmdD9’ ‘~/tmp/scratch/xvfb-run.hzbi8S’
‘~/tmp/scratch/xvfb-run.i0dfun’ ‘~/tmp/scratch/xvfb-run.l05say’
‘~/tmp/scratch/xvfb-run.oAKRPO’ ‘~/tmp/scratch/xvfb-run.sBmmMe’
‘~/tmp/scratch/xvfb-run.tKgABK’ ‘~/tmp/scratch/xvfb-run.ud0jXq’
‘~/tmp/scratch/xvfb-run.v0fF4H’ ‘~/tmp/scratch/xvfb-run.vHwNSv’
‘~/tmp/scratch/xvfb-run.xrrYrg’ ‘~/tmp/scratch/xvfb-run.yGsBm8’
‘~/tmp/scratch/xvfb-run.yzFd2J’ ‘~/.cache/quarto/sass/sass.kv-shm’
‘~/.cache/quarto/sass/sass.kv-wal’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(jointCompRisk)
>
> test_check("jointCompRisk")
Saving _problems/test-basic-32.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-basic.R:32:3'): do_cif_analysis returns formatted summaries ────
Error in `survfit.formula(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)`: the etype argument is no longer supported, use a factor as the status variable
Backtrace:
▆
1. └─jointCompRisk::do_cif_analysis(prepped, tau = 15) at test-basic.R:32:3
2. └─jointCompRisk:::table1_cif(Treatment, Control, tau, 0, 1, 0)
3. └─jointCompRisk:::auc.var.joint(data1, tau, a, b, c)
4. ├─survival::survfit(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)
5. └─survival::survfit.formula(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
Error:
! Test failures.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘Example_analysis.Rmd’ using rmarkdown
Quitting from Example_analysis.Rmd:24-42 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `survfit.formula()`:
! the etype argument is no longer supported, use a factor as the status variable
---
Backtrace:
▆
1. └─jointCompRisk::do_cif_analysis(mydata_std, tau = 15)
2. └─jointCompRisk:::table1_cif(Treatment, Control, tau, 0, 1, 0)
3. └─jointCompRisk:::auc.var.joint(data1, tau, a, b, c)
4. ├─survival::survfit(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)
5. └─survival::survfit.formula(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Example_analysis.Rmd' failed with diagnostics:
the etype argument is no longer supported, use a factor as the status variable
--- failed re-building ‘Example_analysis.Rmd’
--- re-building ‘Vignette.Rmd’ using rmarkdown
main_df package:jointCompRisk R Documentation
_<08>M_<08>a_<08>i_<08>n _<08>C_<08>o_<08>m_<08>p_<08>e_<08>t_<08>i_<08>n_<08>g _<08>R_<08>i_<08>s_<08>k_<08>s _<08>D_<08>a_<08>t_<08>a_<08>s_<08>e_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>e_<08>d _<08>c_<08>l_<08>i_<08>n_<08>i_<08>c_<08>a_<08>l _<08>t_<08>r_<08>i_<08>a_<08>l _<08>d_<08>a_<08>t_<08>a _<08>w_<08>i_<08>t_<08>h
_<08>c_<08>o_<08>m_<08>p_<08>e_<08>t_<08>i_<08>n_<08>g _<08>r_<08>i_<08>s_<08>k_<08>s _<08>s_<08>u_<08>r_<08>v_<08>i_<08>v_<08>a_<08>l _<08>o_<08>u_<08>t_<08>c_<08>o_<08>m_<08>e_<08>s. _<08>T_<08>h_<08>i_<08>s _<08>d_<08>a_<08>t_<08>a_<08>s_<08>e_<08>t _<08>f_<08>o_<08>l_<08>l_<08>o_<08>w_<08>s _<08>t_<08>h_<08>e _<08>s_<08>t_<08>r_<08>u_<08>c_<08>t_<08>u_<08>r_<08>e
_<08>o_<08>f _<08>A_<08>d_<08>a_<08>p_<08>t_<08>i_<08>v_<08>e _<08>C_<08>O_<08>V_<08>I_<08>D-_<08>1_<08>9 _<08>T_<08>r_<08>e_<08>a_<08>t_<08>m_<08>e_<08>n_<08>t _<08>T_<08>r_<08>i_<08>a_<08>l_<08>s (_<08>A_<08>C_<08>T_<08>T) _<08>w_<08>i_<08>t_<08>h _<08>b_<08>u_<08>i_<08>l_<08>t-_<08>i_<08>n _<08>t_<08>r_<08>e_<08>a_<08>t_<08>m_<08>e_<08>n_<08>t
_<08>e_<08>f_<08>f_<08>e_<08>c_<08>t_<08>s _<08>f_<08>o_<08>r _<08>d_<08>e_<08>m_<08>o_<08>n_<08>s_<08>t_<08>r_<08>a_<08>t_<08>i_<08>o_<08>n _<08>p_<08>u_<08>r_<08>p_<08>o_<08>s_<08>e_<08>s.
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Main Competing Risks Dataset Simulated clinical trial data with
competing risks survival outcomes. This dataset follows the
structure of Adaptive COVID-19 Treatment Trials (ACTT) with
built-in treatment effects for demonstration purposes.
_<08>U_<08>s_<08>a_<08>g_<08>e:
data(main_df)
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
A data frame with 150 rows and 7 variables:
ID
Patient identifier (character)
TimeToRecovery
Time to recovery event in days (numeric)
TimeToDeath
Time to death event in days (numeric)
RecoveryCensoringIndicator
Recovery censoring indicator (0=event observed, 1=censored)
DeathCensoringIndicator
Death censoring indicator (0=event observed, 1=censored)
BaselineScore
Baseline severity score, range 4-7 (numeric)
Treatment
Treatment arm indicator (0=control, 1=treatment)
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
This is a simulated dataset created for demonstration purposes
with realistic treatment effects built in: treatment group has
1.5× faster recovery times and 1.8× improved survival compared to
control. The data represents a clinical trial with competing risks
where patients can either recover or die, with administrative
censoring at 30 days.
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
Simulated data based on Weibull distributions with
treatment-specific parameters
_<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
data(main_df)
head(main_df)
summary(main_df)
# Compare outcomes by treatment
tapply(main_df$TimeToRecovery, main_df$Treatment, summary)
tapply(main_df$TimeToDeath, main_df$Treatment, summary)
long_df package:jointCompRisk R Documentation
_<08>L_<08>o_<08>n_<08>g_<08>i_<08>t_<08>u_<08>d_<08>i_<08>n_<08>a_<08>l _<08>S_<08>e_<08>v_<08>e_<08>r_<08>i_<08>t_<08>y _<08>S_<08>c_<08>o_<08>r_<08>e_<08>s _<08>D_<08>a_<08>t_<08>a_<08>s_<08>e_<08>t
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
Repeated measurements of ordinal severity scores over time for the
same patients in the main_df dataset, with treatment-specific
trajectory patterns.
_<08>U_<08>s_<08>a_<08>g_<08>e:
data(long_df)
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
A data frame with variable rows per patient:
PersonID
Patient identifier matching ID in main_df (character)
OrdinalScore
Severity score on 1-8 scale (numeric)
RelativeDay
Study day (numeric) starting from day 0 (baseline)
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
Measurements are taken at scheduled visits: days 0 (baseline), 1,
3, 5, 7, 10, 14, 18, 21, 25, 28. The trajectory follows
treatment-specific probabilities: treatment patients have 45 and
15 worsening probability, creating realistic differential clinical
progression patterns.
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
Simulated data using treatment-specific random walk with
boundaries
_<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
data(long_df)
data(main_df)
head(long_df)
# See data for first patient
subset(long_df, PersonID == "Patient_001")
# Compare average scores by treatment
long_df %>%
dplyr::left_join(main_df[,c("ID","Treatment")], by=c("PersonID"="ID")) %>%
dplyr::group_by(Treatment) %>%
dplyr::summarise(mean_score = mean(OrdinalScore))
Quitting from Vignette.Rmd:159-169 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `survfit.formula()`:
! the etype argument is no longer supported, use a factor as the status variable
---
Backtrace:
▆
1. └─jointCompRisk::do_cif_analysis(mydata_std, tau = 15)
2. └─jointCompRisk:::table1_cif(Treatment, Control, tau, 0, 1, 0)
3. └─jointCompRisk:::auc.var.joint(data1, tau, a, b, c)
4. ├─survival::survfit(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)
5. └─survival::survfit.formula(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
the etype argument is no longer supported, use a factor as the status variable
--- failed re-building ‘Vignette.Rmd’
SUMMARY: processing the following files failed:
‘Example_analysis.Rmd’ ‘Vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.1.1
Check: tests
Result: ERROR
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(jointCompRisk)
>
> test_check("jointCompRisk")
Saving _problems/test-basic-32.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-basic.R:32:3'): do_cif_analysis returns formatted summaries ────
Error in `survfit.formula(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)`: the etype argument is no longer supported, use a factor as the status variable
Backtrace:
▆
1. └─jointCompRisk::do_cif_analysis(prepped, tau = 15) at test-basic.R:32:3
2. └─jointCompRisk:::table1_cif(Treatment, Control, tau, 0, 1, 0)
3. └─jointCompRisk:::auc.var.joint(data1, tau, a, b, c)
4. ├─survival::survfit(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)
5. └─survival::survfit.formula(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
Error:
! Test failures.
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64
Version: 0.1.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'Example_analysis.Rmd' using rmarkdown
Quitting from Example_analysis.Rmd:24-42 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `survfit.formula()`:
! the etype argument is no longer supported, use a factor as the status variable
---
Backtrace:
▆
1. └─jointCompRisk::do_cif_analysis(mydata_std, tau = 15)
2. └─jointCompRisk:::table1_cif(Treatment, Control, tau, 0, 1, 0)
3. └─jointCompRisk:::auc.var.joint(data1, tau, a, b, c)
4. ├─survival::survfit(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)
5. └─survival::survfit.formula(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Example_analysis.Rmd' failed with diagnostics:
the etype argument is no longer supported, use a factor as the status variable
--- failed re-building 'Example_analysis.Rmd'
--- re-building 'Vignette.Rmd' using rmarkdown
Quitting from Vignette.Rmd:159-169 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `survfit.formula()`:
! the etype argument is no longer supported, use a factor as the status variable
---
Backtrace:
▆
1. └─jointCompRisk::do_cif_analysis(mydata_std, tau = 15)
2. └─jointCompRisk:::table1_cif(Treatment, Control, tau, 0, 1, 0)
3. └─jointCompRisk:::auc.var.joint(data1, tau, a, b, c)
4. ├─survival::survfit(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)
5. └─survival::survfit.formula(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
the etype argument is no longer supported, use a factor as the status variable
--- failed re-building 'Vignette.Rmd'
SUMMARY: processing the following files failed:
'Example_analysis.Rmd' 'Vignette.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [4s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(jointCompRisk)
>
> test_check("jointCompRisk")
Saving _problems/test-basic-32.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-basic.R:32:3'): do_cif_analysis returns formatted summaries ────
Error in `survfit.formula(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)`: the etype argument is no longer supported, use a factor as the status variable
Backtrace:
▆
1. └─jointCompRisk::do_cif_analysis(prepped, tau = 15) at test-basic.R:32:3
2. └─jointCompRisk:::table1_cif(Treatment, Control, tau, 0, 1, 0)
3. └─jointCompRisk:::auc.var.joint(data1, tau, a, b, c)
4. ├─survival::survfit(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)
5. └─survival::survfit.formula(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
Error:
! Test failures.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.1.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(jointCompRisk)
>
> test_check("jointCompRisk")
Saving _problems/test-basic-32.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-basic.R:32:3'): do_cif_analysis returns formatted summaries ────
Error in `survfit.formula(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)`: the etype argument is no longer supported, use a factor as the status variable
Backtrace:
▆
1. └─jointCompRisk::do_cif_analysis(prepped, tau = 15) at test-basic.R:32:3
2. └─jointCompRisk:::table1_cif(Treatment, Control, tau, 0, 1, 0)
3. └─jointCompRisk:::auc.var.joint(data1, tau, a, b, c)
4. ├─survival::survfit(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)
5. └─survival::survfit.formula(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.1.1
Check: tests
Result: ERROR
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(jointCompRisk)
>
> test_check("jointCompRisk")
Saving _problems/test-basic-32.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-basic.R:32:3'): do_cif_analysis returns formatted summaries ────
Error in `survfit.formula(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)`: the etype argument is no longer supported, use a factor as the status variable
Backtrace:
▆
1. └─jointCompRisk::do_cif_analysis(prepped, tau = 15) at test-basic.R:32:3
2. └─jointCompRisk:::table1_cif(Treatment, Control, tau, 0, 1, 0)
3. └─jointCompRisk:::auc.var.joint(data1, tau, a, b, c)
4. ├─survival::survfit(Surv(etime, estatus) ~ 1, etype = etype2, data = data.w)
5. └─survival::survfit.formula(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-windows-x86_64