Last updated on 2026-10-23 22:53:12 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.12.0 | 11.94 | 466.12 | 478.06 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.12.0 | 8.42 | 215.95 | 224.37 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.12.0 | 9.00 | 302.55 | 311.55 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.12.0 | 305.83 | OK | |||
| r-devel-windows-x86_64 | 0.12.0 | 20.00 | 478.00 | 498.00 | OK | |
| r-patched-linux-x86_64 | 0.12.0 | 15.46 | 444.02 | 459.48 | OK | |
| r-release-linux-x86_64 | 0.12.0 | 12.60 | 446.07 | 458.67 | OK | |
| r-release-macos-arm64 | 0.12.0 | 3.00 | 113.00 | 116.00 | OK | |
| r-release-macos-x86_64 | 0.12.0 | 9.00 | 522.00 | 531.00 | OK | |
| r-release-windows-x86_64 | 0.12.0 | 15.00 | 466.00 | 481.00 | OK | |
| r-oldrel-macos-arm64 | 0.12.0 | 3.00 | 133.00 | 136.00 | OK | |
| r-oldrel-macos-x86_64 | 0.12.0 | 8.00 | 564.00 | 572.00 | OK | |
| r-oldrel-windows-x86_64 | 0.12.0 | 21.00 | 654.00 | 675.00 | OK |
Version: 0.12.0
Check: examples
Result: ERROR
Running examples in ‘adjustedCurves-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adjusted_curve_diff
> ### Title: Estimate the difference between or the ratio of two
> ### Confounder-Adjusted Survival Curves or CIFs
> ### Aliases: adjusted_curve_diff adjusted_curve_ratio
>
> ### ** Examples
>
> library(adjustedCurves)
> library(survival)
>
> #### Simple Survival Case with adjusted survival curves ####
>
> # simulate some data as example
> set.seed(42)
> sim_dat <- sim_confounded_surv(n=30, max_t=1.2)
> sim_dat$group <- as.factor(sim_dat$group)
>
> # propensity score model
> ps_mod <- glm(group ~ x1 + x2 + x4 + x5, data=sim_dat, family="binomial")
>
> # use it to estimate adjusted survival curves with bootstrapping
> adjsurv <- adjustedsurv(data=sim_dat,
+ variable="group",
+ ev_time="time",
+ event="event",
+ method="iptw_km",
+ treatment_model=ps_mod,
+ conf_int=TRUE,
+ bootstrap=TRUE,
+ n_boot=10) # n_boot should be much higher in reality
>
> # calculate the whole difference curve
> adjdiff <- adjusted_curve_diff(adjsurv)
> adjratio <- adjusted_curve_ratio(adjsurv)
>
> # only some points in time
> adjdiff <- adjusted_curve_diff(adjsurv, times=c(0.2, 0.4))
> adjratio <- adjusted_curve_ratio(adjsurv, times=c(0.2, 0.4))
>
> # with confidence intervals, p-values
> adjdiff <- adjusted_curve_diff(adjsurv, times=c(0.2, 0.4), conf_int=TRUE)
> adjratio <- adjusted_curve_ratio(adjsurv, times=c(0.2, 0.4), conf_int=TRUE)
>
> # using bootstrapping
> adjdiff <- adjusted_curve_diff(adjsurv, times=c(0.2, 0.4), conf_int=TRUE,
+ use_boot=TRUE)
>
> #### Competing Risks Case with adjusted CIFs ####
> if (requireNamespace("cmprsk") & requireNamespace("riskRegression") &
+ requireNamespace("prodlim")) {
+
+ library(cmprsk)
+ library(riskRegression)
+ library(prodlim)
+
+ set.seed(1)
+
+ # simulate some data as example
+ sim_dat <- sim_confounded_crisk(n=100, max_t=1.2)
+ sim_dat$group <- as.factor(sim_dat$group)
+
+ # estimate a cause-specific cox-regression for the outcome
+ csc_mod <- CSC(Hist(time, event) ~ x1 + x2 + x3 + x4 + x5 + x6 + group,
+ data=sim_dat)
+
+ # use it to calculate adjusted CIFs for cause = 1 with bootstrapping
+ adjcif <- adjustedcif(data=sim_dat,
+ variable="group",
+ ev_time="time",
+ event="event",
+ method="direct",
+ outcome_model=csc_mod,
+ conf_int=TRUE,
+ bootstrap=TRUE,
+ n_boot=10,
+ cause=1,
+ product.limit=FALSE)
+
+ # calculate the whole difference curve
+ adjdiff <- adjusted_curve_diff(adjcif)
+ adjratio <- adjusted_curve_ratio(adjcif)
+
+ # with confidence intervals
+ adjdiff <- adjusted_curve_diff(adjcif, conf_int=TRUE)
+ adjratio <- adjusted_curve_ratio(adjcif, conf_int=TRUE)
+
+ # only at specific points in time
+ adjdiff <- adjusted_curve_diff(adjcif, times=c(0.2, 0.4), conf_int=TRUE)
+ adjratio <- adjusted_curve_ratio(adjcif, times=c(0.2, 0.4), conf_int=TRUE)
+ }
Loading required namespace: cmprsk
Loading required namespace: riskRegression
riskRegression version 2026.03.11
Error in a$specials[[i]] : subscript out of bounds
Calls: adjustedcif ... lapply -> FUN -> coxVariableName -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.12.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [96s/134s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(adjustedCurves)
>
> library(dplyr)
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
>
> library(testthat)
> library(vdiffr)
> library(survival)
> library(ggplot2)
> library(Matching)
Loading required package: MASS
Attaching package: 'MASS'
The following object is masked from 'package:dplyr':
select
##
## Matching (Version 4.10-15, Build Date: 2024-10-14)
## See https://www.jsekhon.com for additional documentation.
## Please cite software as:
## Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
## Software with Automated Balance Optimization: The Matching package for R.''
## Journal of Statistical Software, 42(7): 1-52.
##
> library(WeightIt)
> library(prodlim)
> library(MASS)
> library(tidyr)
> library(riskRegression)
riskRegression version 2026.03.11
> library(pec)
Attaching package: 'pec'
The following objects are masked from 'package:riskRegression':
ipcw, selectCox
> library(geepack)
> library(nnet)
> library(cmprsk)
> library(eventglm)
Attaching package: 'eventglm'
The following objects are masked from 'package:prodlim':
leaveOneOut.competing.risks, leaveOneOut.survival
The following objects are masked from 'package:survival':
colon, mgus2
> library(rmarkdown)
> library(mice)
Attaching package: 'mice'
The following object is masked from 'package:stats':
filter
The following objects are masked from 'package:base':
cbind, rbind
>
> test_check("adjustedCurves")
Saving _problems/test_FGR_MI-15.R
Saving _problems/test_FGR_MI-20.R
Saving _problems/test_MI_adjustedcif-39.R
Saving _problems/test_MI_adjustedcif-56.R
Saving _problems/test_MI_adjustedsurv-37.R
Saving _problems/test_MI_adjustedsurv-52.R
Loading required namespace: pammtools
Saving _problems/test_cif_aiptw-28.R
Saving _problems/test_cif_aiptw-43.R
Saving _problems/test_cif_aiptw-60.R
Saving _problems/test_cif_aiptw-78.R
Saving _problems/test_cif_aiptw-99.R
Saving _problems/test_cif_aiptw_pseudo-27.R
Saving _problems/test_cif_aiptw_pseudo-43.R
Saving _problems/test_cif_aiptw_pseudo-61.R
Saving _problems/test_cif_aiptw_pseudo-77.R
Saving _problems/test_cif_aiptw_pseudo-96.R
Saving _problems/test_cif_aiptw_pseudo-116.R
Saving _problems/test_cif_aiptw_pseudo-138.R
Saving _problems/test_cif_aiptw_pseudo-165.R
Saving _problems/test_cif_aiptw_pseudo-181.R
Saving _problems/test_cif_aiptw_pseudo-199.R
Saving _problems/test_cif_aiptw_pseudo-218.R
Saving _problems/test_cif_direct-14.R
Saving _problems/test_cif_direct_pseudo-21.R
Saving _problems/test_cif_direct_pseudo-38.R
Saving _problems/test_cif_direct_pseudo-56.R
Saving _problems/test_cif_direct_pseudo-75.R
Saving _problems/test_cif_direct_pseudo-95.R
Saving _problems/test_cif_direct_pseudo-112.R
Saving _problems/test_cif_direct_pseudo-135.R
Saving _problems/test_cif_direct_pseudo-152.R
Saving _problems/test_cif_direct_pseudo-170.R
Saving _problems/test_cif_direct_pseudo-189.R
Saving _problems/test_cif_g_comp-13.R
Saving _problems/test_cif_iptw-21.R
Saving _problems/test_cif_iptw-35.R
Saving _problems/test_cif_iptw-51.R
Saving _problems/test_cif_iptw-67.R
Saving _problems/test_cif_iptw_pseudo-22.R
Saving _problems/test_cif_iptw_pseudo-36.R
Saving _problems/test_cif_iptw_pseudo-52.R
Saving _problems/test_cif_iptw_pseudo-68.R
Assuming "Treatment" is the treated level. If not, recode the treatment so that 1 is treated and 0 is control.
Saving _problems/test_cif_iptw_pseudo-84.R
Saving _problems/test_cif_iptw_pseudo-99.R
Saving _problems/test_cif_iptw_pseudo-120.R
Saving _problems/test_cif_iptw_pseudo-191.R
Saving _problems/test_cif_iptw_pseudo-215.R
Saving _problems/test_cif_iptw_pseudo-229.R
Saving _problems/test_cif_iptw_pseudo-245.R
Saving _problems/test_cif_iptw_pseudo-261.R
Saving _problems/test_cif_iptw_pseudo-289.R
Loading required namespace: doParallel
starting worker pid=3511173 on localhost:11510 at 15:42:03.116
starting worker pid=3511175 on localhost:11510 at 15:42:03.130
Loading required package: adjustedCurves
loaded adjustedCurves and set parent environment
Loading required package: adjustedCurves
loaded adjustedCurves and set parent environment
Attaching package: ‘mice’
The following object is masked from ‘package:stats’:
filter
The following objects are masked from ‘package:base’:
cbind, rbind
Loading required package: survival
Attaching package: ‘survival’
The following objects are masked from ‘package:eventglm’:
colon, mgus2
Loading required package: prodlim
Attaching package: ‘prodlim’
The following objects are masked from ‘package:eventglm’:
leaveOneOut.competing.risks, leaveOneOut.survival
Attaching package: ‘mice’
The following object is masked from ‘package:stats’:
filter
The following objects are masked from ‘package:base’:
cbind, rbind
Loading required package: survival
Attaching package: ‘survival’
The following objects are masked from ‘package:eventglm’:
colon, mgus2
Loading required package: prodlim
Attaching package: ‘prodlim’
The following objects are masked from ‘package:eventglm’:
leaveOneOut.competing.risks, leaveOneOut.survival
riskRegression version 2026.03.11
Attaching package: ‘riskRegression’
The following objects are masked from ‘package:pec’:
ipcw, selectCox
Loading required package: MASS
##
## Matching (Version 4.10-15, Build Date: 2024-10-14)
## See https://www.jsekhon.com for additional documentation.
## Please cite software as:
## Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
## Software with Automated Balance Optimization: The Matching package for R.''
## Journal of Statistical Software, 42(7): 1-52.
##
Attaching package: ‘dplyr’
The following object is masked from ‘package:MASS’:
select
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Loading required package: foreach
Loading required package: rngtools
riskRegression version 2026.03.11
Attaching package: ‘riskRegression’
The following objects are masked from ‘package:pec’:
ipcw, selectCox
Loading required package: MASS
##
## Matching (Version 4.10-15, Build Date: 2024-10-14)
## See https://www.jsekhon.com for additional documentation.
## Please cite software as:
## Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
## Software with Automated Balance Optimization: The Matching package for R.''
## Journal of Statistical Software, 42(7): 1-52.
##
Attaching package: ‘dplyr’
The following object is masked from ‘package:MASS’:
select
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Loading required package: foreach
Loading required package: rngtools
starting worker pid=3517354 on localhost:11510 at 15:42:09.382
starting worker pid=3517355 on localhost:11510 at 15:42:09.470
Loading required package: adjustedCurves
loaded adjustedCurves and set parent environment
Loading required package: adjustedCurves
loaded adjustedCurves and set parent environment
Attaching package: ‘mice’
The following object is masked from ‘package:stats’:
filter
The following objects are masked from ‘package:base’:
cbind, rbind
Loading required package: survival
Attaching package: ‘mice’
The following object is masked from ‘package:stats’:
filter
The following objects are masked from ‘package:base’:
cbind, rbind
Attaching package: ‘survival’
The following objects are masked from ‘package:eventglm’:
colon, mgus2
Loading required package: prodlim
Loading required package: survival
Attaching package: ‘survival’
The following objects are masked from ‘package:eventglm’:
colon, mgus2
Loading required package: prodlim
Attaching package: ‘prodlim’
The following objects are masked from ‘package:eventglm’:
leaveOneOut.competing.risks, leaveOneOut.survival
Attaching package: ‘prodlim’
The following objects are masked from ‘package:eventglm’:
leaveOneOut.competing.risks, leaveOneOut.survival
riskRegression version 2026.03.11
Attaching package: ‘riskRegression’
The following objects are masked from ‘package:pec’:
ipcw, selectCox
Loading required package: MASS
##
## Matching (Version 4.10-15, Build Date: 2024-10-14)
## See https://www.jsekhon.com for additional documentation.
## Please cite software as:
## Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
## Software with Automated Balance Optimization: The Matching package for R.''
## Journal of Statistical Software, 42(7): 1-52.
##
Attaching package: ‘dplyr’
riskRegression version 2026.03.11
Attaching package: ‘riskRegression’
The following objects are masked from ‘package:pec’:
ipcw, selectCox
Loading required package: MASS
##
## Matching (Version 4.10-15, Build Date: 2024-10-14)
## See https://www.jsekhon.com for additional documentation.
## Please cite software as:
## Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
## Software with Automated Balance Optimization: The Matching package for R.''
## Journal of Statistical Software, 42(7): 1-52.
##
Attaching package: ‘dplyr’
The following object is masked from ‘package:MASS’:
select
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Loading required package: foreach
Loading required package: rngtools
The following object is masked from ‘package:MASS’:
select
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Loading required package: foreach
Loading required package: rngtools
starting worker pid=3524261 on localhost:11510 at 15:42:15.420
starting worker pid=3524257 on localhost:11510 at 15:42:15.439
Loading required package: adjustedCurves
loaded adjustedCurves and set parent environment
Loading required package: adjustedCurves
loaded adjustedCurves and set parent environment
Attaching package: ‘mice’
The following object is masked from ‘package:stats’:
filter
The following objects are masked from ‘package:base’:
cbind, rbind
Loading required package: survival
Attaching package: ‘survival’
The following objects are masked from ‘package:eventglm’:
colon, mgus2
Loading required package: prodlim
Attaching package: ‘mice’
The following object is masked from ‘package:stats’:
filter
The following objects are masked from ‘package:base’:
cbind, rbind
Loading required package: survival
Attaching package: ‘survival’
The following objects are masked from ‘package:eventglm’:
colon, mgus2
Loading required package: prodlim
Attaching package: ‘prodlim’
The following objects are masked from ‘package:eventglm’:
leaveOneOut.competing.risks, leaveOneOut.survival
Attaching package: ‘prodlim’
The following objects are masked from ‘package:eventglm’:
leaveOneOut.competing.risks, leaveOneOut.survival
riskRegression version 2026.03.11
Attaching package: ‘riskRegression’
The following objects are masked from ‘package:pec’:
ipcw, selectCox
riskRegression version 2026.03.11
Attaching package: ‘riskRegression’
The following objects are masked from ‘package:pec’:
ipcw, selectCox
Loading required package: MASS
##
## Matching (Version 4.10-15, Build Date: 2024-10-14)
## See https://www.jsekhon.com for additional documentation.
## Please cite software as:
## Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
## Software with Automated Balance Optimization: The Matching package for R.''
## Journal of Statistical Software, 42(7): 1-52.
##
Attaching package: ‘dplyr’
The following object is masked from ‘package:MASS’:
select
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Loading required package: foreach
Loading required package: rngtools
Loading required package: MASS
##
## Matching (Version 4.10-15, Build Date: 2024-10-14)
## See https://www.jsekhon.com for additional documentation.
## Please cite software as:
## Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
## Software with Automated Balance Optimization: The Matching package for R.''
## Journal of Statistical Software, 42(7): 1-52.
##
Attaching package: ‘dplyr’
The following object is masked from ‘package:MASS’:
select
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Loading required package: foreach
Loading required package: rngtools
starting worker pid=3530272 on localhost:11510 at 15:42:20.833
starting worker pid=3530273 on localhost:11510 at 15:42:20.835
Loading required package: adjustedCurves
loaded adjustedCurves and set parent environment
Loading required package: adjustedCurves
loaded adjustedCurves and set parent environment
Attaching package: ‘mice’
The following object is masked from ‘package:stats’:
filter
The following objects are masked from ‘package:base’:
cbind, rbind
Loading required package: survival
Attaching package: ‘survival’
The following objects are masked from ‘package:eventglm’:
colon, mgus2
Loading required package: prodlim
Attaching package: ‘prodlim’
The following objects are masked from ‘package:eventglm’:
leaveOneOut.competing.risks, leaveOneOut.survival
Attaching package: ‘mice’
The following object is masked from ‘package:stats’:
filter
The following objects are masked from ‘package:base’:
cbind, rbind
Loading required package: survival
Attaching package: ‘survival’
The following objects are masked from ‘package:eventglm’:
colon, mgus2
Loading required package: prodlim
Attaching package: ‘prodlim’
The following objects are masked from ‘package:eventglm’:
leaveOneOut.competing.risks, leaveOneOut.survival
riskRegression version 2026.03.11
Attaching package: ‘riskRegression’
The following objects are masked from ‘package:pec’:
ipcw, selectCox
Loading required package: MASS
##
## Matching (Version 4.10-15, Build Date: 2024-10-14)
## See https://www.jsekhon.com for additional documentation.
## Please cite software as:
## Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
## Software with Automated Balance Optimization: The Matching package for R.''
## Journal of Statistical Software, 42(7): 1-52.
##
Attaching package: ‘dplyr’
The following object is masked from ‘package:MASS’:
select
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Loading required package: foreach
Loading required package: rngtools
riskRegression version 2026.03.11
Attaching package: ‘riskRegression’
The following objects are masked from ‘package:pec’:
ipcw, selectCox
Loading required package: MASS
##
## Matching (Version 4.10-15, Build Date: 2024-10-14)
## See https://www.jsekhon.com for additional documentation.
## Please cite software as:
## Jasjeet S. Sekhon. 2011. ``Multivariate and Propensity Score Matching
## Software with Automated Balance Optimization: The Matching package for R.''
## Journal of Statistical Software, 42(7): 1-52.
##
Attaching package: ‘dplyr’
The following object is masked from ‘package:MASS’:
select
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Loading required package: foreach
Loading required package: rngtools
Saving _problems/test_general_stuff-268.R
Saving _problems/test_general_stuff-308.R
Loading required namespace: cowplot
Loading required namespace: ggpp
Saving _problems/test_surv_aiptw-27.R
Saving _problems/test_surv_aiptw-41.R
Saving _problems/test_surv_aiptw-57.R
Saving _problems/test_surv_aiptw-74.R
Saving _problems/test_surv_aiptw-94.R
Saving _problems/test_surv_aiptw_pseudo-27.R
Saving _problems/test_surv_aiptw_pseudo-42.R
Saving _problems/test_surv_aiptw_pseudo-59.R
Saving _problems/test_surv_aiptw_pseudo-77.R
Saving _problems/test_surv_aiptw_pseudo-96.R
Saving _problems/test_surv_aiptw_pseudo-112.R
Saving _problems/test_surv_aiptw_pseudo-137.R
Saving _problems/test_surv_aiptw_pseudo-152.R
Saving _problems/test_surv_aiptw_pseudo-169.R
Saving _problems/test_surv_aiptw_pseudo-187.R
Saving _problems/test_surv_direct-22.R
Saving _problems/test_surv_direct-35.R
Saving _problems/test_surv_direct-50.R
Saving _problems/test_surv_direct-65.R
Saving _problems/test_surv_direct-81.R
Saving _problems/test_surv_direct-107.R
Saving _problems/test_surv_direct-120.R
Saving _problems/test_surv_direct-135.R
Saving _problems/test_surv_direct-150.R
Saving _problems/test_surv_direct-166.R
Saving _problems/test_surv_direct-186.R
Saving _problems/test_surv_direct_pseudo-20.R
Saving _problems/test_surv_direct_pseudo-36.R
Saving _problems/test_surv_direct_pseudo-53.R
Saving _problems/test_surv_direct_pseudo-71.R
Saving _problems/test_surv_direct_pseudo-90.R
Saving _problems/test_surv_direct_pseudo-104.R
Saving _problems/test_surv_direct_pseudo-120.R
Saving _problems/test_surv_direct_pseudo-137.R
Saving _problems/test_surv_direct_pseudo-155.R
Saving _problems/test_surv_iptw_cens-22.R
Saving _problems/test_surv_iptw_cens-38.R
Assuming "Treatment" is the treated level. If not, recode the treatment so that 1 is treated and 0 is control.
Saving _problems/test_surv_iptw_cens-54.R
Assuming "Treatment" is the treated level. If not, supply an argument to `focal`.
Saving _problems/test_surv_iptw_cens-71.R
Saving _problems/test_surv_iptw_cens-103.R
Saving _problems/test_surv_iptw_cens-120.R
Saving _problems/test_surv_iptw_cens-136.R
Saving _problems/test_surv_iptw_cens-159.R
Saving _problems/test_surv_iptw_cens-190.R
Saving _problems/test_surv_iptw_cox-22.R
Saving _problems/test_surv_iptw_cox-37.R
Assuming "Treatment" is the treated level. If not, recode the treatment so that 1 is treated and 0 is control.
Saving _problems/test_surv_iptw_cox-52.R
Saving _problems/test_surv_iptw_cox-66.R
Saving _problems/test_surv_iptw_cox-86.R
Saving _problems/test_surv_iptw_cox-148.R
Saving _problems/test_surv_iptw_cox-163.R
Saving _problems/test_surv_iptw_cox-190.R
Assuming "Treatment" is the treated level. If not, recode the treatment so that 1 is treated and 0 is control.
Assuming "Treatment" is the treated level. If not, supply an argument to `focal`.
Assuming "Treatment" is the treated level. If not, recode the treatment so that 1 is treated and 0 is control.
Assuming "Treatment" is the treated level. If not, recode the treatment so that 1 is treated and 0 is control.
Saving _problems/test_surv_iptw_pseudo-21.R
Saving _problems/test_surv_iptw_pseudo-34.R
Saving _problems/test_surv_iptw_pseudo-49.R
Saving _problems/test_surv_iptw_pseudo-64.R
Assuming "Treatment" is the treated level. If not, recode the treatment so that 1 is treated and 0 is control.
Saving _problems/test_surv_iptw_pseudo-79.R
Saving _problems/test_surv_iptw_pseudo-93.R
Saving _problems/test_surv_iptw_pseudo-128.R
Saving _problems/test_surv_iptw_pseudo-196.R
Saving _problems/test_surv_iptw_pseudo-209.R
Saving _problems/test_surv_iptw_pseudo-224.R
Saving _problems/test_surv_iptw_pseudo-239.R
Saving _problems/test_surv_iptw_pseudo-266.R
Saving _problems/test_surv_iv_2SRIF-47.R
Saving _problems/test_surv_iv_2SRIF-61.R
Saving _problems/test_surv_iv_2SRIF-73.R
Saving _problems/test_surv_iv_2SRIF-85.R
Saving _problems/test_surv_iv_2SRIF-97.R
[ FAIL 124 | WARN 0 | SKIP 171 | PASS 1013 ]
══ Skipped tests (171) ═════════════════════════════════════════════════════════
• On CRAN (171): 'test_MI_adjustedcif.r:64:1', 'test_MI_adjustedsurv.r:60:1',
'test_adjusted_curve_test.r:43:1', 'test_adjusted_curve_test.r:88:1',
'test_adjusted_curve_test.r:138:1', 'test_adjusted_curve_test.r:190:1',
'test_adjustedcif.method_S3.r:15:1', 'test_adjustedcif.method_S3.r:19:1',
'test_adjustedcif_S3.r:17:1', 'test_adjustedcif_S3.r:21:1',
'test_adjustedcif_S3.r:26:1', 'test_adjustedcif_S3.r:31:1',
'test_adjustedcif_S3.r:36:1', 'test_adjustedcif_S3.r:41:1',
'test_adjustedcif_S3.r:46:1', 'test_adjustedcif_S3.r:51:1',
'test_adjustedcif_S3.r:56:1', 'test_adjustedcif_S3.r:61:1',
'test_adjustedcif_S3.r:67:1', 'test_adjustedcif_S3.r:73:1',
'test_adjustedcif_S3.r:79:1', 'test_adjustedsurv.method_S3.r:15:1',
'test_adjustedsurv_S3.r:16:1', 'test_adjustedsurv_S3.r:20:1',
'test_adjustedsurv_S3.r:25:1', 'test_adjustedsurv_S3.r:30:1',
'test_adjustedsurv_S3.r:35:1', 'test_adjustedsurv_S3.r:40:1',
'test_adjustedsurv_S3.r:45:1', 'test_adjustedsurv_S3.r:50:1',
'test_adjustedsurv_S3.r:55:1', 'test_adjustedsurv_S3.r:60:1',
'test_adjustedsurv_S3.r:65:1', 'test_adjustedsurv_S3.r:70:1',
'test_adjustedsurv_S3.r:75:1', 'test_adjustedsurv_S3.r:80:1',
'test_adjustedsurv_S3.r:85:1', 'test_adjustedsurv_S3.r:90:1',
'test_adjustedsurv_S3.r:95:1', 'test_adjustedsurv_S3.r:100:1',
'test_adjustedsurv_S3.r:106:1', 'test_adjustedsurv_S3.r:112:1',
'test_adjustedsurv_S3.r:118:1', 'test_curve_test_S3.r:20:1',
'test_curve_test_S3.r:24:1', 'test_plot.adjustedcif.r:19:1',
'test_plot.adjustedcif.r:25:1', 'test_plot.adjustedcif.r:31:1',
'test_plot.adjustedcif.r:37:1', 'test_plot.adjustedcif.r:43:1',
'test_plot.adjustedcif.r:54:1', 'test_plot.adjustedcif.r:65:1',
'test_plot.adjustedcif.r:81:1', 'test_plot.adjustedcif.r:97:1',
'test_plot.adjustedcif.r:103:1', 'test_plot.adjustedcif.r:109:1',
'test_plot.adjustedcif.r:115:1', 'test_plot.adjustedcif.r:121:1',
'test_plot.adjustedcif.r:128:1', 'test_plot.adjustedcif.r:134:1',
'test_plot.adjustedcif.r:140:1', 'test_plot.adjustedcif.r:151:1',
'test_plot.adjustedcif.r:157:1', 'test_plot.adjustedcif.r:163:1',
'test_plot.adjustedcif.r:169:1', 'test_plot.adjustedcif.r:176:1',
'test_plot.adjustedcif.r:182:1', 'test_plot.adjustedcif.r:188:1',
'test_plot.adjustedcif.r:195:1', 'test_plot.adjustedsurv.r:35:1',
'test_plot.adjustedsurv.r:41:1', 'test_plot.adjustedsurv.r:47:1',
'test_plot.adjustedsurv.r:53:1', 'test_plot.adjustedsurv.r:59:1',
'test_plot.adjustedsurv.r:70:1', 'test_plot.adjustedsurv.r:81:1',
'test_plot.adjustedsurv.r:97:1', 'test_plot.adjustedsurv.r:113:1',
'test_plot.adjustedsurv.r:123:1', 'test_plot.adjustedsurv.r:129:1',
'test_plot.adjustedsurv.r:135:1', 'test_plot.adjustedsurv.r:141:1',
'test_plot.adjustedsurv.r:147:1', 'test_plot.adjustedsurv.r:154:1',
'test_plot.adjustedsurv.r:160:1', 'test_plot.adjustedsurv.r:166:1',
'test_plot.adjustedsurv.r:172:1', 'test_plot.adjustedsurv.r:178:1',
'test_plot.adjustedsurv.r:189:1', 'test_plot.adjustedsurv.r:196:1',
'test_plot.adjustedsurv.r:202:1', 'test_plot.adjustedsurv.r:208:1',
'test_plot.adjustedsurv.r:215:1', 'test_plot.adjustedsurv.r:222:1',
'test_plot.adjustedsurv.r:230:1', 'test_plot.adjustedsurv.r:267:1',
'test_plot.adjustedsurv.r:273:1', 'test_plot.adjustedsurv.r:279:1',
'test_plot.adjustedsurv.r:286:1', 'test_plot.adjustedsurv.r:292:1',
'test_plot.adjustedsurv.r:299:1', 'test_plot.adjustedsurv.r:306:1',
'test_plot.adjustedsurv.r:312:1', 'test_plot.adjustedsurv.r:318:1',
'test_plot.adjustedsurv.r:326:1', 'test_plot.adjustedsurv.r:335:1',
'test_plot.adjustedsurv.r:341:1', 'test_plot.adjustedsurv.r:348:1',
'test_plot.adjustedsurv.r:354:1', 'test_plot.adjustedsurv.r:362:1',
'test_plot.adjustedsurv.r:371:1', 'test_plot.adjustedsurv.r:378:1',
'test_plot.adjustedsurv.r:389:1', 'test_plot.adjustedsurv.r:395:1',
'test_plot.adjustedsurv.r:402:1', 'test_plot.adjustedsurv.r:410:1',
'test_plot.adjustedsurv.r:436:1', 'test_plot.adjustedsurv.r:443:1',
'test_plot.adjustedsurv.r:450:1', 'test_plot.adjustedsurv.r:457:1',
'test_plot_auc_curve.r:19:1', 'test_plot_auc_curve.r:25:1',
'test_plot_auc_curve.r:31:1', 'test_plot_auc_curve.r:37:1',
'test_plot_auc_curve.r:43:1', 'test_plot_auc_curve.r:49:1',
'test_plot_auc_curve.r:56:1', 'test_plot_auc_curve.r:62:1',
'test_plot_auc_curve.r:68:1', 'test_plot_auc_curve.r:74:1',
'test_plot_auc_curve.r:80:1', 'test_plot_auc_curve.r:87:1',
'test_plot_auc_curve.r:94:1', 'test_plot_auc_curve.r:100:1',
'test_plot_auc_curve.r:106:1', 'test_plot_auc_curve.r:112:1',
'test_plot_auc_curve.r:119:1', 'test_plot_auc_curve.r:125:1',
'test_plot_auc_curve.r:131:1', 'test_plot_auc_curve.r:137:1',
'test_plot_curve_diff.r:18:1', 'test_plot_curve_diff.r:24:1',
'test_plot_curve_diff.r:30:1', 'test_plot_curve_diff.r:38:1',
'test_plot_curve_diff.r:44:1', 'test_plot_curve_diff.r:50:1',
'test_plot_curve_diff.r:58:1', 'test_plot_curve_diff.r:64:1',
'test_plot_curve_diff.r:70:1', 'test_plot_curve_diff.r:76:1',
'test_plot_curve_diff.r:82:1', 'test_plot_curve_diff.r:88:1',
'test_plot_curve_diff.r:95:1', 'test_plot_curve_diff.r:102:1',
'test_plot_curve_diff.r:108:1', 'test_plot_curve_diff.r:114:1',
'test_plot_curve_diff.r:120:1', 'test_plot_curve_diff.r:126:1',
'test_plot_curve_diff.r:138:1', 'test_plot_curve_diff.r:144:1',
'test_plot_curve_diff.r:150:1', 'test_plot_curve_diff.r:172:1',
'test_plot_curve_ratio.r:18:1', 'test_plot_curve_ratio.r:24:1',
'test_plot_curve_ratio.r:30:1', 'test_plot_curve_ratio.r:36:1',
'test_plot_curve_ratio.r:42:1', 'test_plot_curve_ratio.r:48:1',
'test_plot_curve_ratio.r:54:1', 'test_plot_curve_ratio.r:71:1',
'test_surv_prox_aiptw.r:72:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_FGR_MI.r:15:3'): no additional args ────────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::FGR_MI(...) at test_FGR_MI.r:15:3
2. └─adjustedCurves:::ce_model_mi(...)
3. └─riskRegression::FGR(...)
4. └─prodlim::EventHistory.frame(...)
5. └─prodlim::model.design(...)
6. └─stats::delete.response(terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test_FGR_MI.r:20:3'): with additional args ──────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::FGR_MI(...) at test_FGR_MI.r:20:3
2. └─adjustedCurves:::ce_model_mi(...)
3. └─riskRegression::FGR(...)
4. └─prodlim::EventHistory.frame(...)
5. └─prodlim::model.design(...)
6. └─stats::delete.response(terms)
7. └─stats (local) off(a$specials[[i]])
── Error ('test_MI_adjustedcif.r:32:3'): MI, direct, no boot ───────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_MI_adjustedcif.r:32:3
2. ├─base::do.call(adjustedcif, args = args2)
3. └─adjustedCurves (local) `<fn>`(...)
4. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
5. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
6. │ └─base::do.call(.fcn, args = args, envir = envir)
7. └─adjustedCurves (local) `<fn>`(...)
8. └─riskRegression::ate(...)
9. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
10. └─riskRegression (local) `<fn>`(...)
11. ├─riskRegression::predictRisk(...)
12. └─riskRegression:::predictRisk.CauseSpecificCox(...)
13. ├─stats::predict(...)
14. └─riskRegression:::predict.CauseSpecificCox(...)
15. └─riskRegression:::compressData(...)
16. └─base::lapply(...)
17. └─riskRegression (local) FUN(X[[i]], ...)
18. └─riskRegression::coxVariableName(iO, model.frame = coxModelFrame(iO))
19. └─stats::delete.response(...)
20. └─stats (local) off(a$specials[[i]])
── Error ('test_MI_adjustedcif.r:47:3'): MI, direct, boot ──────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test_MI_adjustedcif.r:46:3
2. │ └─base::withCallingHandlers(...)
3. └─adjustedCurves::adjustedcif(...) at test_MI_adjustedcif.r:47:3
4. ├─base::do.call(adjustedcif, args = args2)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::adjustedcif_boot(...)
7. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
8. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
9. │ └─base::do.call(.fcn, args = args, envir = envir)
10. └─adjustedCurves (local) `<fn>`(...)
11. └─riskRegression::ate(...)
12. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
13. └─riskRegression (local) `<fn>`(...)
14. ├─riskRegression::predictRisk(...)
15. └─riskRegression:::predictRisk.CauseSpecificCox(...)
16. ├─stats::predict(...)
17. └─riskRegression:::predict.CauseSpecificCox(...)
18. └─riskRegression:::compressData(...)
19. └─base::lapply(...)
20. └─riskRegression (local) FUN(X[[i]], ...)
21. └─riskRegression::coxVariableName(iO, model.frame = coxModelFrame(iO))
22. └─stats::delete.response(...)
23. └─stats (local) off(a$specials[[i]])
── Error ('test_MI_adjustedsurv.r:31:3'): MI, direct, no boot ──────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_MI_adjustedsurv.r:31:3
2. ├─base::do.call(adjustedsurv, args = args2)
3. └─adjustedCurves (local) `<fn>`(...)
4. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
6. │ └─base::do.call(.fcn, args = args, envir = envir)
7. └─adjustedCurves (local) `<fn>`(...)
8. └─riskRegression::ate(...)
9. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
10. └─riskRegression (local) `<fn>`(...)
11. ├─riskRegression::predictRisk(...)
12. └─riskRegression:::predictRisk.coxph(...)
13. └─riskRegression::predictCox(...)
14. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
15. └─stats::delete.response(...)
16. └─stats (local) off(a$specials[[i]])
── Error ('test_MI_adjustedsurv.r:44:3'): MI, direct, boot ─────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_MI_adjustedsurv.r:44:3
2. ├─base::do.call(adjustedsurv, args = args2)
3. └─adjustedCurves (local) `<fn>`(...)
4. └─adjustedCurves:::adjustedsurv_boot(...)
5. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
6. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
7. │ └─base::do.call(.fcn, args = args, envir = envir)
8. └─adjustedCurves (local) `<fn>`(...)
9. └─riskRegression::ate(...)
10. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
11. └─riskRegression (local) `<fn>`(...)
12. ├─riskRegression::predictRisk(...)
13. └─riskRegression:::predictRisk.coxph(...)
14. └─riskRegression::predictCox(...)
15. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
16. └─stats::delete.response(...)
17. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_aiptw.r:20:3'): 2 treatments, no conf_int, no boot ─────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_aiptw.r:20:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─riskRegression::ate(...)
7. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
8. └─riskRegression (local) `<fn>`(...)
9. └─base::lapply(...)
10. └─riskRegression (local) FUN(X[[i]], ...)
11. ├─riskRegression::predictRisk(...)
12. └─riskRegression:::predictRisk.coxph(...)
13. └─riskRegression::predictCox(...)
14. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
15. └─stats::delete.response(...)
16. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_aiptw.r:35:3'): 2 treatments, with conf_int, no boot ───────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_aiptw.r:35:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─riskRegression::ate(...)
7. ├─riskRegression::iidCox(...)
8. └─riskRegression:::iidCox.CauseSpecificCox(...)
9. ├─riskRegression::iidCox(...)
10. └─riskRegression:::iidCox.coxph(...)
11. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
12. └─stats::delete.response(...)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_aiptw.r:50:3'): 2 treatments, no conf_int, with boot ───────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_aiptw.r:50:3
2. └─adjustedCurves:::adjustedcif_boot(...)
3. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─riskRegression::ate(...)
8. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
9. └─riskRegression (local) `<fn>`(...)
10. └─base::lapply(...)
11. └─riskRegression (local) FUN(X[[i]], ...)
12. ├─riskRegression::predictRisk(...)
13. └─riskRegression:::predictRisk.coxph(...)
14. └─riskRegression::predictCox(...)
15. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
16. └─stats::delete.response(...)
17. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_aiptw.r:67:3'): 2 treatments, no conf_int, no boot, with times ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_aiptw.r:67:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─riskRegression::ate(...)
7. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
8. └─riskRegression (local) `<fn>`(...)
9. └─base::lapply(...)
10. └─riskRegression (local) FUN(X[[i]], ...)
11. ├─riskRegression::predictRisk(...)
12. └─riskRegression:::predictRisk.coxph(...)
13. └─riskRegression::predictCox(...)
14. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
15. └─stats::delete.response(...)
16. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_aiptw.r:87:3'): 2 treatments, no conf_int, no boot, with times, with cens_mod ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_aiptw.r:87:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─riskRegression::ate(...)
7. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
8. └─riskRegression (local) `<fn>`(...)
9. └─base::lapply(...)
10. └─riskRegression (local) FUN(X[[i]], ...)
11. ├─riskRegression::predictRisk(...)
12. └─riskRegression:::predictRisk.coxph(...)
13. └─riskRegression::predictCox(...)
14. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
15. └─stats::delete.response(...)
16. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_aiptw_pseudo.r:18:3'): 2 treatments, no conf_int, no boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_aiptw_pseudo.r:18:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_aiptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_aiptw_pseudo.r:34:3'): 2 treatments, with conf_int, no boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_aiptw_pseudo.r:34:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_aiptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_aiptw_pseudo.r:50:3'): 2 treatments, no conf_int, with boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_aiptw_pseudo.r:50:3
2. └─adjustedCurves:::adjustedcif_boot(...)
3. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_aiptw_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_aiptw_pseudo.r:68:3'): 2 treatments, using propensity score directly ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_aiptw_pseudo.r:68:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_aiptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_aiptw_pseudo.r:84:3'): 2 treatments, no conf_int, no boot, with times, factor time ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_aiptw_pseudo.r:84:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_aiptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_aiptw_pseudo.r:103:3'): 2 treatments, no conf_int, no boot, with times, ns time ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_aiptw_pseudo.r:103:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_aiptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_aiptw_pseudo.r:127:3'): works with survival data ───────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test_cif_aiptw_pseudo.r:127:3
2. │ └─base::withCallingHandlers(...)
3. └─adjustedCurves::adjustedcif(...)
4. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
5. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
6. │ └─base::do.call(.fcn, args = args, envir = envir)
7. └─adjustedCurves (local) `<fn>`(...)
8. └─adjustedCurves:::method_aiptw_pseudo(...)
9. └─adjustedCurves:::calc_pseudo_surv(...)
10. ├─prodlim::jackknife(...)
11. └─prodlim::prodlim(hist_formula, data = data)
12. └─prodlim::EventHistory.frame(...)
13. └─prodlim::model.design(...)
14. └─stats::delete.response(terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_aiptw_pseudo.r:156:3'): > 2 treatments, no conf_int, no boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_aiptw_pseudo.r:156:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_aiptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_aiptw_pseudo.r:172:3'): > 2 treatments, with conf_int, no boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_aiptw_pseudo.r:172:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_aiptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_aiptw_pseudo.r:188:3'): > 2 treatments, no conf_int, with boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_aiptw_pseudo.r:188:3
2. └─adjustedCurves:::adjustedcif_boot(...)
3. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_aiptw_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_aiptw_pseudo.r:206:3'): > 2 treatments, no conf_int, no boot, with times, factor time ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_aiptw_pseudo.r:206:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_aiptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_direct.r:13:1'): (code run outside of `test_that()`) ───────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─riskRegression::FGR(...) at test_cif_direct.r:13:1
2. └─prodlim::EventHistory.frame(...)
3. └─prodlim::model.design(...)
4. └─stats::delete.response(terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_direct_pseudo.r:13:3'): 2 treatments, no conf_int, no boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_direct_pseudo.r:13:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_direct_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_direct_pseudo.r:28:3'): 2 treatments, no conf_int, with boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_direct_pseudo.r:28:3
2. └─adjustedCurves:::adjustedcif_boot(...)
3. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_direct_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_direct_pseudo.r:45:3'): 2 treatments, no conf_int, no boot, with times ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_direct_pseudo.r:45:3
2. └─adjustedCurves:::adjustedcif_boot(...)
3. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_direct_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_direct_pseudo.r:64:3'): 2 treatments, no conf_int, no boot, with times, type_time='factor' ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_direct_pseudo.r:64:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_direct_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_direct_pseudo.r:83:5'): 2 treatments, no conf_int, no boot, with times, type_time='ns' ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_direct_pseudo.r:83:5
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_direct_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_direct_pseudo.r:102:3'): 2 treatments, no conf_int, no boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test_cif_direct_pseudo.r:102:3
2. │ └─base::withCallingHandlers(...)
3. └─adjustedCurves::adjustedcif(...)
4. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
5. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
6. │ └─base::do.call(.fcn, args = args, envir = envir)
7. └─adjustedCurves (local) `<fn>`(...)
8. └─adjustedCurves:::method_direct_pseudo(...)
9. └─adjustedCurves:::calc_pseudo_surv(...)
10. ├─prodlim::jackknife(...)
11. └─prodlim::prodlim(hist_formula, data = data)
12. └─prodlim::EventHistory.frame(...)
13. └─prodlim::model.design(...)
14. └─stats::delete.response(terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_direct_pseudo.r:127:3'): > 2 treatments, no conf_int, no boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_direct_pseudo.r:127:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_direct_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_direct_pseudo.r:142:3'): > 2 treatments, no conf_int, with boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_direct_pseudo.r:142:3
2. └─adjustedCurves:::adjustedcif_boot(...)
3. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_direct_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_direct_pseudo.r:159:3'): > 2 treatments, no conf_int, no boot, with times ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_direct_pseudo.r:159:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_direct_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_direct_pseudo.r:178:3'): > 2 treatments, no conf_int, no boot, with times, type_time='factor' ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_direct_pseudo.r:178:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_direct_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_g_comp.r:13:1'): (code run outside of `test_that()`) ───────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─riskRegression::FGR(...) at test_cif_g_comp.r:13:1
2. └─prodlim::EventHistory.frame(...)
3. └─prodlim::model.design(...)
4. └─stats::delete.response(terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_iptw.r:14:3'): 2 treatments, no conf_int, no boot ──────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_iptw.r:14:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─riskRegression::ate(...)
7. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
8. └─riskRegression (local) `<fn>`(...)
9. └─base::lapply(...)
10. └─riskRegression (local) FUN(X[[i]], ...)
11. ├─riskRegression::predictRisk(...)
12. └─riskRegression:::predictRisk.coxph(...)
13. └─riskRegression::predictCox(...)
14. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
15. └─stats::delete.response(...)
16. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_iptw.r:28:3'): 2 treatments, with conf_int, no boot ────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_iptw.r:28:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─riskRegression::ate(...)
7. ├─riskRegression::iidCox(...)
8. └─riskRegression:::iidCox.coxph(...)
9. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
10. └─stats::delete.response(...)
11. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_iptw.r:42:3'): 2 treatments, no conf_int, with boot ────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_iptw.r:42:3
2. └─adjustedCurves:::adjustedcif_boot(...)
3. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─riskRegression::ate(...)
8. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
9. └─riskRegression (local) `<fn>`(...)
10. └─base::lapply(...)
11. └─riskRegression (local) FUN(X[[i]], ...)
12. ├─riskRegression::predictRisk(...)
13. └─riskRegression:::predictRisk.coxph(...)
14. └─riskRegression::predictCox(...)
15. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
16. └─stats::delete.response(...)
17. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_iptw.r:58:3'): 2 treatments, with conf_int, with boot ──────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_iptw.r:58:3
2. └─adjustedCurves:::adjustedcif_boot(...)
3. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─riskRegression::ate(...)
8. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
9. └─riskRegression (local) `<fn>`(...)
10. └─base::lapply(...)
11. └─riskRegression (local) FUN(X[[i]], ...)
12. ├─riskRegression::predictRisk(...)
13. └─riskRegression:::predictRisk.coxph(...)
14. └─riskRegression::predictCox(...)
15. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
16. └─stats::delete.response(...)
17. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_iptw_pseudo.r:15:3'): 2 treatments, no conf_int, no boot ───
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_iptw_pseudo.r:15:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_iptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_iptw_pseudo.r:29:3'): 2 treatments, with conf_int, no boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_iptw_pseudo.r:29:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_iptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_iptw_pseudo.r:43:3'): 2 treatments, no conf_int, with boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_iptw_pseudo.r:43:3
2. └─adjustedCurves:::adjustedcif_boot(...)
3. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_iptw_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_iptw_pseudo.r:59:3'): 2 treatments, with conf_int, with boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_iptw_pseudo.r:59:3
2. └─adjustedCurves:::adjustedcif_boot(...)
3. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_iptw_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_iptw_pseudo.r:75:3'): 2 treatments, no conf_int, with WeightIt ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_iptw_pseudo.r:75:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_iptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_iptw_pseudo.r:91:3'): 2 treatments, no conf_int, with user-weights ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_iptw_pseudo.r:91:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_iptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_iptw_pseudo.r:111:3'): 3 ways of iptw calculation are equal ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_iptw_pseudo.r:111:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_iptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_iptw_pseudo.r:182:3'): works with survival data ────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test_cif_iptw_pseudo.r:182:3
2. │ └─base::withCallingHandlers(...)
3. └─adjustedCurves::adjustedcif(...)
4. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
5. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
6. │ └─base::do.call(.fcn, args = args, envir = envir)
7. └─adjustedCurves (local) `<fn>`(...)
8. └─adjustedCurves:::method_iptw_pseudo(...)
9. └─adjustedCurves:::calc_pseudo_surv(...)
10. ├─prodlim::jackknife(...)
11. └─prodlim::prodlim(hist_formula, data = data)
12. └─prodlim::EventHistory.frame(...)
13. └─prodlim::model.design(...)
14. └─stats::delete.response(terms)
15. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_iptw_pseudo.r:208:3'): > 2 treatments, no conf_int, no boot, no ... ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_iptw_pseudo.r:208:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_iptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_iptw_pseudo.r:222:3'): > 2 treatments, with conf_int, no boot, no ... ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_iptw_pseudo.r:222:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_iptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_iptw_pseudo.r:236:3'): > 2 treatments, no conf_int, with boot, no ... ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_iptw_pseudo.r:236:3
2. └─adjustedCurves:::adjustedcif_boot(...)
3. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_iptw_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_iptw_pseudo.r:252:3'): > 2 treatments, with conf_int, with boot, no ... ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_iptw_pseudo.r:252:3
2. └─adjustedCurves:::adjustedcif_boot(...)
3. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_iptw_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_cif_iptw_pseudo.r:281:3'): > 2 treatments, no conf_int, with user-weights ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedcif(...) at test_cif_iptw_pseudo.r:281:3
2. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_iptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_general_stuff.r:104:3'): adjustedsurv, aiptw, with n_cores = 2 ──
Error in `{ { rngtools::RNGseed(.doRNG.stream) } { adjustedsurv_boot(data = data, variable = variable, ev_time = ev_time, event = event, method = method, times = times, i = i, surv_fun = surv_fun, na.action = na.action, force_bounds = force_bounds, iso_reg = iso_reg, ...) } }`: task 1 failed - "subscript out of bounds"
Backtrace:
▆
1. ├─adjustedCurves:::quiet(...) at test_general_stuff.r:104:3
2. │ └─base::force(x)
3. └─adjustedCurves::adjustedsurv(...)
4. ├─... %dorng% ...
5. │ └─base::do.call(`%dopar%`, list(obj, ex), envir = parent.frame())
6. └─foreach (local) `<fn>`(...)
7. └─e$fun(obj, substitute(ex), parent.frame(), e$data)
── Error ('test_general_stuff.r:143:3'): adjustedcif, aiptw, with n_cores = 2 ──
Error in `{ { rngtools::RNGseed(.doRNG.stream) } { adjustedcif_boot(data = data, variable = variable, ev_time = ev_time, event = event, method = method, times = times, i = i, cif_fun = cif_fun, cause = cause, na.action = na.action, force_bounds = force_bounds, iso_reg = iso_reg, ...) } }`: task 1 failed - "subscript out of bounds"
Backtrace:
▆
1. ├─adjustedCurves:::quiet(...) at test_general_stuff.r:143:3
2. │ └─base::force(x)
3. ├─base::suppressWarnings(...)
4. │ └─base::withCallingHandlers(...)
5. └─adjustedCurves::adjustedcif(...)
6. ├─... %dorng% ...
7. │ └─base::do.call(`%dopar%`, list(obj, ex), envir = parent.frame())
8. └─foreach (local) `<fn>`(...)
9. └─e$fun(obj, substitute(ex), parent.frame(), e$data)
── Error ('test_general_stuff.r:257:3'): adjustedsurv, using force_bounds and iso_reg with bootstrapping ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_general_stuff.r:257:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_iptw_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_general_stuff.r:296:3'): adjustedcif, using force_bounds and iso_reg with bootstrapping ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test_general_stuff.r:296:3
2. │ └─base::withCallingHandlers(...)
3. └─adjustedCurves::adjustedcif(...)
4. └─adjustedCurves:::adjustedcif_boot(...)
5. ├─R.utils::doCall(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
6. ├─R.utils::doCall.default(cif_fun, args = args, .ignoreUnusedArgs = FALSE)
7. │ └─base::do.call(.fcn, args = args, envir = envir)
8. └─adjustedCurves (local) `<fn>`(...)
9. └─adjustedCurves:::method_iptw_pseudo(...)
10. └─adjustedCurves:::calc_pseudo_surv(...)
11. ├─prodlim::jackknife(...)
12. └─prodlim::prodlim(hist_formula, data = data)
13. └─prodlim::EventHistory.frame(...)
14. └─prodlim::model.design(...)
15. └─stats::delete.response(terms)
16. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_aiptw.r:20:3'): 2 treatments, no conf_int, no boot ────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_aiptw.r:20:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::cif_aiptw(...)
7. └─riskRegression::ate(...)
8. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
9. └─riskRegression (local) `<fn>`(...)
10. └─base::lapply(...)
11. └─riskRegression (local) FUN(X[[i]], ...)
12. ├─riskRegression::predictRisk(...)
13. └─riskRegression:::predictRisk.coxph(...)
14. └─riskRegression::predictCox(...)
15. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
16. └─stats::delete.response(...)
17. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_aiptw.r:34:3'): 2 treatments, with conf_int, no boot ──────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_aiptw.r:34:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::cif_aiptw(...)
7. └─riskRegression::ate(...)
8. ├─riskRegression::iidCox(...)
9. └─riskRegression:::iidCox.coxph(...)
10. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
11. └─stats::delete.response(...)
12. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_aiptw.r:48:3'): 2 treatments, no conf_int, with boot ──────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_aiptw.r:48:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::cif_aiptw(...)
8. └─riskRegression::ate(...)
9. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
10. └─riskRegression (local) `<fn>`(...)
11. └─base::lapply(...)
12. └─riskRegression (local) FUN(X[[i]], ...)
13. ├─riskRegression::predictRisk(...)
14. └─riskRegression:::predictRisk.coxph(...)
15. └─riskRegression::predictCox(...)
16. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
17. └─stats::delete.response(...)
18. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_aiptw.r:64:3'): 2 treatments, no conf_int, no boot, with times ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_aiptw.r:64:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::cif_aiptw(...)
7. └─riskRegression::ate(...)
8. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
9. └─riskRegression (local) `<fn>`(...)
10. └─base::lapply(...)
11. └─riskRegression (local) FUN(X[[i]], ...)
12. ├─riskRegression::predictRisk(...)
13. └─riskRegression:::predictRisk.coxph(...)
14. └─riskRegression::predictCox(...)
15. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
16. └─stats::delete.response(...)
17. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_aiptw.r:83:3'): 2 treatments, no conf_int, no boot, with times, with cens_mod ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_aiptw.r:83:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::cif_aiptw(...)
7. └─riskRegression::ate(...)
8. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
9. └─riskRegression (local) `<fn>`(...)
10. └─base::lapply(...)
11. └─riskRegression (local) FUN(X[[i]], ...)
12. ├─riskRegression::predictRisk(...)
13. └─riskRegression:::predictRisk.coxph(...)
14. └─riskRegression::predictCox(...)
15. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
16. └─stats::delete.response(...)
17. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_aiptw_pseudo.r:19:3'): 2 treatments, no conf_int, no boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_aiptw_pseudo.r:19:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_aiptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_aiptw_pseudo.r:34:3'): 2 treatments, with conf_int, no boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_aiptw_pseudo.r:34:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_aiptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_aiptw_pseudo.r:49:3'): 2 treatments, no conf_int, with boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_aiptw_pseudo.r:49:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_aiptw_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_aiptw_pseudo.r:66:3'): 2 treatments, no conf_int, no boot, with times, factor time ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_aiptw_pseudo.r:66:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_aiptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_aiptw_pseudo.r:84:3'): 2 treatments, no conf_int, no boot, with times, ns time ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_aiptw_pseudo.r:84:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_aiptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_aiptw_pseudo.r:103:3'): 2 treatments, with ps_scores supplied ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_aiptw_pseudo.r:103:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_aiptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_aiptw_pseudo.r:129:3'): > 2 treatments, no conf_int, no boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_aiptw_pseudo.r:129:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_aiptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_aiptw_pseudo.r:144:3'): > 2 treatments, with conf_int, no boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_aiptw_pseudo.r:144:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_aiptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_aiptw_pseudo.r:159:3'): > 2 treatments, no conf_int, with boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_aiptw_pseudo.r:159:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_aiptw_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_aiptw_pseudo.r:176:3'): > 2 treatments, no conf_int, no boot, with times, factor time ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_aiptw_pseudo.r:176:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_aiptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct.r:16:3'): 2 treatments, no conf_int, no boot ───────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct.r:16:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─riskRegression::ate(...)
7. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
8. └─riskRegression (local) `<fn>`(...)
9. ├─riskRegression::predictRisk(...)
10. └─riskRegression:::predictRisk.coxph(...)
11. └─riskRegression::predictCox(...)
12. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
13. └─stats::delete.response(...)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct.r:29:3'): 2 treatments, with conf_int, no boot ─────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct.r:29:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─riskRegression::ate(...)
7. ├─riskRegression::iidCox(...)
8. └─riskRegression:::iidCox.coxph(...)
9. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
10. └─stats::delete.response(...)
11. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct.r:42:3'): 2 treatments, no conf_int, with boot ─────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct.r:42:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─riskRegression::ate(...)
8. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
9. └─riskRegression (local) `<fn>`(...)
10. ├─riskRegression::predictRisk(...)
11. └─riskRegression:::predictRisk.coxph(...)
12. └─riskRegression::predictCox(...)
13. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
14. └─stats::delete.response(...)
15. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct.r:57:3'): 2 treatments, with conf_int, with boot ───
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct.r:57:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─riskRegression::ate(...)
8. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
9. └─riskRegression (local) `<fn>`(...)
10. ├─riskRegression::predictRisk(...)
11. └─riskRegression:::predictRisk.coxph(...)
12. └─riskRegression::predictCox(...)
13. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
14. └─stats::delete.response(...)
15. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct.r:72:3'): 2 treatments, no conf_int, no boot, with times ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct.r:72:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─riskRegression::ate(...)
8. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
9. └─riskRegression (local) `<fn>`(...)
10. ├─riskRegression::predictRisk(...)
11. └─riskRegression:::predictRisk.coxph(...)
12. └─riskRegression::predictCox(...)
13. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
14. └─stats::delete.response(...)
15. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct.r:101:3'): > 2 treatments, no conf_int, no boot ────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct.r:101:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─riskRegression::ate(...)
7. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
8. └─riskRegression (local) `<fn>`(...)
9. ├─riskRegression::predictRisk(...)
10. └─riskRegression:::predictRisk.coxph(...)
11. └─riskRegression::predictCox(...)
12. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
13. └─stats::delete.response(...)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct.r:114:3'): > 2 treatments, with conf_int, no boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct.r:114:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─riskRegression::ate(...)
7. ├─riskRegression::iidCox(...)
8. └─riskRegression:::iidCox.coxph(...)
9. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
10. └─stats::delete.response(...)
11. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct.r:127:3'): > 2 treatments, no conf_int, with boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct.r:127:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─riskRegression::ate(...)
8. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
9. └─riskRegression (local) `<fn>`(...)
10. ├─riskRegression::predictRisk(...)
11. └─riskRegression:::predictRisk.coxph(...)
12. └─riskRegression::predictCox(...)
13. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
14. └─stats::delete.response(...)
15. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct.r:142:3'): > 2 treatments, with conf_int, with boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct.r:142:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─riskRegression::ate(...)
8. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
9. └─riskRegression (local) `<fn>`(...)
10. ├─riskRegression::predictRisk(...)
11. └─riskRegression:::predictRisk.coxph(...)
12. └─riskRegression::predictCox(...)
13. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
14. └─stats::delete.response(...)
15. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct.r:157:3'): > 2 treatments, no conf_int, no boot, with times ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct.r:157:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─riskRegression::ate(...)
7. ├─base::do.call(fct.pointEstimate, args.pointEstimate)
8. └─riskRegression (local) `<fn>`(...)
9. ├─riskRegression::predictRisk(...)
10. └─riskRegression:::predictRisk.coxph(...)
11. └─riskRegression::predictCox(...)
12. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
13. └─stats::delete.response(...)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct.r:184:1'): (code run outside of `test_that()`) ─────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─riskRegression::riskRegression(...) at test_surv_direct.r:184:1
2. └─prodlim::EventHistory.frame(...)
3. └─prodlim::model.design(...)
4. └─stats::delete.response(terms)
5. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct_pseudo.r:13:3'): 2 treatments, no conf_int, no boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct_pseudo.r:13:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_direct_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct_pseudo.r:27:3'): 2 treatments, no conf_int, with boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct_pseudo.r:27:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_direct_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct_pseudo.r:43:3'): 2 treatments, no conf_int, no boot, with times ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct_pseudo.r:43:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_direct_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct_pseudo.r:61:3'): 2 treatments, no conf_int, no boot, with times, type_time='factor' ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct_pseudo.r:61:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_direct_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct_pseudo.r:79:5'): 2 treatments, no conf_int, no boot, with times, type_time='ns' ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct_pseudo.r:79:5
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_direct_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct_pseudo.r:97:3'): > 2 treatments, no conf_int, no boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct_pseudo.r:97:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_direct_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct_pseudo.r:111:3'): > 2 treatments, no conf_int, with boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct_pseudo.r:111:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_direct_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct_pseudo.r:127:3'): > 2 treatments, no conf_int, no boot, with times ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct_pseudo.r:127:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_direct_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_direct_pseudo.r:145:3'): > 2 treatments, no conf_int, no boot, with times, type_time='factor' ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_direct_pseudo.r:145:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_direct_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_cens.r:15:3'): 2 treatments, no conf_int, no boot ────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_cens.r:15:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::fit_censoring_model(...)
7. └─survival::basehaz(fit, centered = FALSE)
8. ├─survival::survfit(fit, se.fit = FALSE)
9. └─survival:::survfit.coxph(fit, se.fit = FALSE)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_cens.r:29:3'): 2 treatments, no conf_int, with boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_cens.r:29:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::fit_censoring_model(...)
8. └─survival::basehaz(fit, centered = FALSE)
9. ├─survival::survfit(fit, se.fit = FALSE)
10. └─survival:::survfit.coxph(fit, se.fit = FALSE)
11. └─survival:::model.matrix.coxph(object, data = mf)
12. └─stats::delete.response(object$terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_cens.r:45:3'): 2 treatments, no conf_int, with WeightIt ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_cens.r:45:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::fit_censoring_model(...)
7. └─survival::basehaz(fit, centered = FALSE)
8. ├─survival::survfit(fit, se.fit = FALSE)
9. └─survival:::survfit.coxph(fit, se.fit = FALSE)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_cens.r:61:3'): 2 treatments, no conf_int, with WeightIt + additional args ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_cens.r:61:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::fit_censoring_model(...)
7. └─survival::basehaz(fit, centered = FALSE)
8. ├─survival::survfit(fit, se.fit = FALSE)
9. └─survival:::survfit.coxph(fit, se.fit = FALSE)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_cens.r:95:3'): 2 treatments, no conf_int, with user-weights ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_cens.r:95:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::fit_censoring_model(...)
7. └─survival::basehaz(fit, centered = FALSE)
8. ├─survival::survfit(fit, se.fit = FALSE)
9. └─survival:::survfit.coxph(fit, se.fit = FALSE)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_cens.r:110:3'): use trim_quantiles ───────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_cens.r:110:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::fit_censoring_model(...)
8. └─survival::basehaz(fit, centered = FALSE)
9. ├─survival::survfit(fit, se.fit = FALSE)
10. └─survival:::survfit.coxph(fit, se.fit = FALSE)
11. └─survival:::model.matrix.coxph(object, data = mf)
12. └─stats::delete.response(object$terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_cens.r:125:3'): changing the Cox model specification ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_cens.r:125:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::fit_censoring_model(...)
8. └─survival::basehaz(fit, centered = FALSE)
9. ├─survival::survfit(fit, se.fit = FALSE)
10. └─survival:::survfit.coxph(fit, se.fit = FALSE)
11. └─survival:::model.matrix.coxph(object, data = mf)
12. └─stats::delete.response(object$terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_cens.r:152:3'): > 2 treatments, no conf_int, no boot, no ... ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_cens.r:152:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::fit_censoring_model(...)
7. └─survival::basehaz(fit, centered = FALSE)
8. ├─survival::survfit(fit, se.fit = FALSE)
9. └─survival:::survfit.coxph(fit, se.fit = FALSE)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_cens.r:182:3'): > 2 treatments, no conf_int, with user-weights ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_cens.r:182:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::fit_censoring_model(...)
7. └─survival::basehaz(fit, centered = FALSE)
8. ├─survival::survfit(fit, se.fit = FALSE)
9. └─survival:::survfit.coxph(fit, se.fit = FALSE)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_cox.r:16:3'): 2 treatments, no boot ──────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_cox.r:16:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. ├─survival::survfit(model, se.fit = FALSE, conf.int = conf_level)
7. └─survival:::survfit.coxph(model, se.fit = FALSE, conf.int = conf_level)
8. └─survival:::model.matrix.coxph(object, data = mf)
9. └─stats::delete.response(object$terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_cox.r:29:3'): 2 treatments, with boot ────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_cox.r:29:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. ├─survival::survfit(model, se.fit = FALSE, conf.int = conf_level)
8. └─survival:::survfit.coxph(model, se.fit = FALSE, conf.int = conf_level)
9. └─survival:::model.matrix.coxph(object, data = mf)
10. └─stats::delete.response(object$terms)
11. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_cox.r:44:3'): 2 treatments, with WeightIt ────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_cox.r:44:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. ├─survival::survfit(model, se.fit = FALSE, conf.int = conf_level)
7. └─survival:::survfit.coxph(model, se.fit = FALSE, conf.int = conf_level)
8. └─survival:::model.matrix.coxph(object, data = mf)
9. └─stats::delete.response(object$terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_cox.r:59:3'): 2 treatments, with user-weights ────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_cox.r:59:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. ├─survival::survfit(model, se.fit = FALSE, conf.int = conf_level)
7. └─survival:::survfit.coxph(model, se.fit = FALSE, conf.int = conf_level)
8. └─survival:::model.matrix.coxph(object, data = mf)
9. └─stats::delete.response(object$terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_cox.r:78:3'): 3 ways of iptw calculation are equal ───
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_cox.r:78:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. ├─survival::survfit(model, se.fit = FALSE, conf.int = conf_level)
7. └─survival:::survfit.coxph(model, se.fit = FALSE, conf.int = conf_level)
8. └─survival:::model.matrix.coxph(object, data = mf)
9. └─stats::delete.response(object$terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_cox.r:142:3'): > 2 treatments, no boot, no ... ───────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_cox.r:142:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. ├─survival::survfit(model, se.fit = FALSE, conf.int = conf_level)
7. └─survival:::survfit.coxph(model, se.fit = FALSE, conf.int = conf_level)
8. └─survival:::model.matrix.coxph(object, data = mf)
9. └─stats::delete.response(object$terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_cox.r:155:3'): > 2 treatments, with boot, no ... ─────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_cox.r:155:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. ├─survival::survfit(model, se.fit = FALSE, conf.int = conf_level)
8. └─survival:::survfit.coxph(model, se.fit = FALSE, conf.int = conf_level)
9. └─survival:::model.matrix.coxph(object, data = mf)
10. └─stats::delete.response(object$terms)
11. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_cox.r:183:3'): > 2 treatments, with user-weights ─────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_cox.r:183:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. ├─survival::survfit(model, se.fit = FALSE, conf.int = conf_level)
7. └─survival:::survfit.coxph(model, se.fit = FALSE, conf.int = conf_level)
8. └─survival:::model.matrix.coxph(object, data = mf)
9. └─stats::delete.response(object$terms)
10. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_pseudo.r:15:3'): 2 treatments, no conf_int, no boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_pseudo.r:15:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_iptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_pseudo.r:28:3'): 2 treatments, with conf_int, no boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_pseudo.r:28:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_iptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_pseudo.r:41:3'): 2 treatments, no conf_int, with boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_pseudo.r:41:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_iptw_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_pseudo.r:56:3'): 2 treatments, with conf_int, with boot ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_pseudo.r:56:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_iptw_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_pseudo.r:71:3'): 2 treatments, no conf_int, with WeightIt ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_pseudo.r:71:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_iptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_pseudo.r:86:3'): 2 treatments, no conf_int, with user-weights ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_pseudo.r:86:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_iptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_pseudo.r:120:3'): 3 ways of iptw calculation are equal ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_pseudo.r:120:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_iptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_pseudo.r:190:3'): > 2 treatments, no conf_int, no boot, no ... ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_pseudo.r:190:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_iptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_pseudo.r:203:3'): > 2 treatments, with conf_int, no boot, no ... ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_pseudo.r:203:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_iptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_pseudo.r:216:3'): > 2 treatments, no conf_int, with boot, no ... ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_pseudo.r:216:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_iptw_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_pseudo.r:231:3'): > 2 treatments, with conf_int, with boot, no ... ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_pseudo.r:231:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─adjustedCurves:::method_iptw_pseudo(...)
8. └─adjustedCurves:::calc_pseudo_surv(...)
9. ├─prodlim::jackknife(...)
10. └─prodlim::prodlim(hist_formula, data = data)
11. └─prodlim::EventHistory.frame(...)
12. └─prodlim::model.design(...)
13. └─stats::delete.response(terms)
14. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iptw_pseudo.r:259:3'): > 2 treatments, no conf_int, with user-weights ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iptw_pseudo.r:259:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─adjustedCurves:::method_iptw_pseudo(...)
7. └─adjustedCurves:::calc_pseudo_surv(...)
8. ├─prodlim::jackknife(...)
9. └─prodlim::prodlim(hist_formula, data = data)
10. └─prodlim::EventHistory.frame(...)
11. └─prodlim::model.design(...)
12. └─stats::delete.response(terms)
13. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iv_2SRIF.r:41:3'): general case ───────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iv_2SRIF.r:41:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─survival::basehaz(cox_tsrif, centered = FALSE)
7. ├─survival::survfit(fit, se.fit = FALSE)
8. └─survival:::survfit.coxph(fit, se.fit = FALSE)
9. └─survival:::model.matrix.coxph(object, data = mf)
10. └─stats::delete.response(object$terms)
11. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iv_2SRIF.r:53:3'): with bootstrapping ─────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iv_2SRIF.r:53:3
2. └─adjustedCurves:::adjustedsurv_boot(...)
3. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
5. │ └─base::do.call(.fcn, args = args, envir = envir)
6. └─adjustedCurves (local) `<fn>`(...)
7. └─survival::basehaz(cox_tsrif, centered = FALSE)
8. ├─survival::survfit(fit, se.fit = FALSE)
9. └─survival:::survfit.coxph(fit, se.fit = FALSE)
10. └─survival:::model.matrix.coxph(object, data = mf)
11. └─stats::delete.response(object$terms)
12. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iv_2SRIF.r:67:3'): multiple adjust_vars ───────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iv_2SRIF.r:67:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─survival::basehaz(cox_tsrif, centered = FALSE)
7. ├─survival::survfit(fit, se.fit = FALSE)
8. └─survival:::survfit.coxph(fit, se.fit = FALSE)
9. └─survival:::model.matrix.coxph(object, data = mf)
10. └─stats::delete.response(object$terms)
11. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iv_2SRIF.r:79:3'): multiple adjust_vars with a factor variable ──
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iv_2SRIF.r:79:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─survival::basehaz(cox_tsrif, centered = FALSE)
7. ├─survival::survfit(fit, se.fit = FALSE)
8. └─survival:::survfit.coxph(fit, se.fit = FALSE)
9. └─survival:::model.matrix.coxph(object, data = mf)
10. └─stats::delete.response(object$terms)
11. └─stats (local) off(a$specials[[i]])
── Error ('test_surv_iv_2SRIF.r:91:3'): no adjust_vars ─────────────────────────
<subscriptOutOfBoundsError/error/condition>
Error in `a$specials[[i]]`: subscript out of bounds
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...) at test_surv_iv_2SRIF.r:91:3
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─survival::basehaz(cox_tsrif, centered = FALSE)
7. ├─survival::survfit(fit, se.fit = FALSE)
8. └─survival:::survfit.coxph(fit, se.fit = FALSE)
9. └─survival:::model.matrix.coxph(object, data = mf)
10. └─stats::delete.response(object$terms)
11. └─stats (local) off(a$specials[[i]])
[ FAIL 124 | WARN 0 | SKIP 171 | PASS 1013 ]
Error:
! Test failures.
Warning messages:
1: In for (i in ind) init <- forceAndCall(2, f, init, x[[i]]) :
closing unused connection 7 (<-localhost:11510)
2: In for (i in ind) init <- forceAndCall(2, f, init, x[[i]]) :
closing unused connection 6 (<-localhost:11510)
Execution halted
Error in unserialize(node$con) :
error reading from connection '->localhost:11510'
Calls: <Anonymous> ... doTryCatch -> recvData -> recvData.SOCKnode -> unserialize
In addition: Warning messages:
1: In coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1 ; coefficient may be infinite.
2: In ate_checkArgs(call = call, object.event = object.event, object.censor = object.censor, :
Rare event
Execution halted
Error in unserialize(node$con) :
error reading from connection '->localhost:11510'
Calls: <Anonymous> ... doTryCatch -> recvData -> recvData.SOCKnode -> unserialize
In addition: Warning messages:
1: In coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
2: In coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1 ; coefficient may be infinite.
3: In ate_checkArgs(call = call, object.event = object.event, object.censor = object.censor, :
Rare event
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.12.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘adjustedCurves.Rmd’ using rmarkdown
Quitting from adjustedCurves.Rmd:72-80 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `a$specials[[i]]`:
! subscript out of bounds
---
Backtrace:
▆
1. └─adjustedCurves::adjustedsurv(...)
2. ├─R.utils::doCall(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
3. ├─R.utils::doCall.default(surv_fun, args = args, .ignoreUnusedArgs = FALSE)
4. │ └─base::do.call(.fcn, args = args, envir = envir)
5. └─adjustedCurves (local) `<fn>`(...)
6. └─riskRegression::ate(...)
7. ├─riskRegression::iidCox(...)
8. └─riskRegression:::iidCox.coxph(...)
9. └─riskRegression::coxVariableName(object, model.frame = object.modelFrame)
10. └─stats::delete.response(...)
11. └─stats (local) off(a$specials[[i]])
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'adjustedCurves.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘adjustedCurves.Rmd’
--- re-building ‘comparing_groups.rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘comparing_groups.rmd’
--- re-building ‘faq.rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘faq.rmd’
--- re-building ‘method_overview.rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘method_overview.rmd’
--- re-building ‘plot_customization.rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘plot_customization.rmd’
SUMMARY: processing the following file failed:
‘adjustedCurves.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc