Last updated on 2026-07-09 14:00:45 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.1 | 8.50 | 125.91 | 134.41 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.1 | 6.04 | 87.42 | 93.46 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.1.1 | 16.00 | 103.80 | 119.80 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.1 | 14.00 | 88.16 | 102.16 | ERROR | |
| r-devel-windows-x86_64 | 0.1.1 | 11.00 | 121.00 | 132.00 | OK | |
| r-patched-linux-x86_64 | 0.1.1 | 8.99 | 119.66 | 128.65 | OK | |
| r-release-linux-x86_64 | 0.1.1 | 7.27 | 120.93 | 128.20 | OK | |
| 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 | 10.00 | 122.00 | 132.00 | OK | |
| 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 | 15.00 | 167.00 | 182.00 | OK |
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