Last updated on 2026-10-24 01:51:42 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.0 | 2.42 | 37.10 | 39.52 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2.0 | 2.01 | 28.47 | 30.48 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.0 | 30.99 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.0 | 25.04 | OK | |||
| r-devel-windows-x86_64 | 0.2.0 | 5.00 | 58.00 | 63.00 | OK | |
| r-patched-linux-x86_64 | 0.2.0 | 2.56 | 32.83 | 35.39 | OK | |
| r-release-linux-x86_64 | 0.2.0 | 2.81 | 32.80 | 35.61 | OK | |
| r-release-macos-arm64 | 0.2.0 | 1.00 | 12.00 | 13.00 | OK | |
| r-release-macos-x86_64 | 0.2.0 | 2.00 | 37.00 | 39.00 | OK | |
| r-release-windows-x86_64 | 0.2.0 | 6.00 | 57.00 | 63.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.0 | OK | ||||
| r-oldrel-macos-x86_64 | 0.2.0 | 2.00 | 40.00 | 42.00 | OK | |
| r-oldrel-windows-x86_64 | 0.2.0 | 6.00 | 64.00 | 70.00 | OK |
Version: 0.2.0
Check: examples
Result: ERROR
Running examples in ‘pmcalibration-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pmcalibration
> ### Title: Create a calibration curve
> ### Aliases: pmcalibration
>
> ### ** Examples
>
> # binary outcome -------------------------------------
> library(pmcalibration)
> # simulate some data
> n <- 500
> dat <- sim_dat(N = n, a1 = .5, a3 = .2)
> head(dat)
x1 x2 y LP
1 -0.6264538 0.07730312 1 -0.05883606
2 0.1836433 -0.29686864 0 0.37587109
3 -0.8356286 -1.18324224 1 -1.32112064
4 1.5952808 0.01129269 1 2.11017649
5 0.3295078 0.99160104 1 1.88645686
6 -0.8204684 1.59396745 1 1.01193909
> # predictions
> p <- with(dat, invlogit(.5 + x1 + x2 + x1*x2*.1))
>
> # fit calibration curve
> cal <- pmcalibration(y = dat$y, p = p, smooth = "gam", k = 20, ci = "pw")
>
> summary(cal)
Calibration metrics based on a calibration curve estimated for a binary outcome via a generalized additive model (see ?mgcv::s) using logit transformed predicted probabilities.
Estimate
Eavg 0.022
E50 0.025
E90 0.033
Emax 0.034
ECI 0.058
>
> plot(cal)
>
> # time to event outcome -------------------------------------
> library(pmcalibration)
> if (requireNamespace("survival", quietly = TRUE)){
+ library(survival)
+
+ data('transplant', package="survival")
+ transplant <- na.omit(transplant)
+ transplant = subset(transplant, futime > 0)
+ transplant$ltx <- as.numeric(transplant$event == "ltx")
+
+ # get predictions from coxph model at time = 100
+ # note that as we are fitting and evaluating the model on the same data
+ cph <- coxph(Surv(futime, ltx) ~ age + sex + abo + year, data = transplant)
+
+ time <- 100
+ newd <- transplant; newd$futime <- time; newd$ltx <- 1
+ p <- 1 - exp(-predict(cph, type = "expected", newdata=newd))
+ y <- with(transplant, Surv(futime, ltx))
+
+ cal <- pmcalibration(y = y, p = p, smooth = "rcs", nk=5, ci = "pw", time = time)
+
+ summary(cal)
+
+ plot(cal)
+
+ }
Error in a$specials[[i]] : subscript out of bounds
Calls: predict ... model.matrix -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc