Last updated on 2026-10-24 09:50:51 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.1 | 26.21 | 138.51 | 164.72 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 1.0.1 | 19.61 | 89.29 | 108.90 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.1 | 21.00 | 92.05 | 113.05 | NOTE | |
| r-devel-linux-x86_64-fedora-gcc | 1.0.1 | 21.00 | 95.14 | 116.14 | NOTE | |
| r-devel-windows-x86_64 | 1.0.1 | 32.00 | 238.00 | 270.00 | NOTE | |
| r-patched-linux-x86_64 | 1.0.1 | 27.10 | 125.13 | 152.23 | NOTE | |
| r-release-linux-x86_64 | 1.0.1 | 27.76 | 126.07 | 153.83 | NOTE | |
| r-release-macos-arm64 | 1.0.1 | 7.00 | 34.00 | 41.00 | NOTE | |
| r-release-macos-x86_64 | 1.0.1 | 18.00 | 184.00 | 202.00 | NOTE | |
| r-release-windows-x86_64 | 1.0.1 | 33.00 | 166.00 | 199.00 | NOTE | |
| r-oldrel-macos-arm64 | 1.0.1 | NOTE | ||||
| r-oldrel-macos-x86_64 | 1.0.1 | 16.00 | 113.00 | 129.00 | NOTE | |
| r-oldrel-windows-x86_64 | 1.0.1 | 43.00 | 208.00 | 251.00 | NOTE |
Version: 1.0.1
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Theodor Adrian Balan <hello@tbalan.com>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = c("Theodor", "Adrian"),
family = "Balan",
role = c("aut", "cre"),
email = "hello@tbalan.com"),
person(given = "Hein",
family = "Putter",
role = "aut"))
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.0.1
Check: Rd files
Result: NOTE
checkRd: (-1) emfrail_control.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) emfrail_control.Rd:55-57: Lost braces in \itemize; meant \describe ?
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.0.1
Check: examples
Result: ERROR
Running examples in ‘frailtyEM-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary.emfrail
> ### Title: Summary for 'emfrail' objects
> ### Aliases: summary.emfrail
>
> ### ** Examples
>
> data("bladder")
Warning in data("bladder") : data set ‘bladder’ not found
> mod_gamma <- emfrail(Surv(start, stop, status) ~ treatment + cluster(id), bladder1)
Warning in Surv(start, stop, status) :
Stop time must be > start time, NA created
Warning in Surv(start, stop, status) :
Invalid status value, converted to NA
Warning in Surv(start, stop, status) :
Stop time must be > start time, NA created
Warning in Surv(start, stop, status) :
Invalid status value, converted to NA
> summary(mod_gamma)
Call:
emfrail(formula = Surv(start, stop, status) ~ treatment + cluster(id),
data = bladder1)
Regression coefficients:
coef exp(coef) se(coef) adj. se z p
treatmentpyridoxine 0.141 1.151 0.339 0.339 0.415 0.68
treatmentthiotepa -0.159 0.853 0.331 0.331 -0.480 0.63
Estimated distribution: gamma / left truncation: FALSE
Fit summary:
Commenges-Andersen test for heterogeneity: p-val 4.08e-18
no-frailty Log-likelihood: -800.212
Log-likelihood: -763.58
LRT: 1/2 * pchisq(73.3), p-val 5.67e-18
Frailty summary:
estimate lower 95% upper 95%
Var[Z] 1.197 0.717 1.921
Kendall's tau 0.374 0.264 0.490
Median concordance 0.377 0.261 0.501
E[logZ] -0.707 -1.212 -0.399
Var[logZ] 2.152 1.031 4.607
theta 0.835 0.521 1.395
Confidence intervals based on the likelihood function
> summary(mod_gamma, print_opts = list(frailty_verbose = FALSE))
Call:
emfrail(formula = Surv(start, stop, status) ~ treatment + cluster(id),
data = bladder1)
Regression coefficients:
coef exp(coef) se(coef) adj. se z p
treatmentpyridoxine 0.141 1.151 0.339 0.339 0.415 0.68
treatmentthiotepa -0.159 0.853 0.331 0.331 -0.480 0.63
Estimated distribution: gamma / left truncation: FALSE
Fit summary:
Commenges-Andersen test for heterogeneity: p-val 4.08e-18
no-frailty Log-likelihood: -800.212
Log-likelihood: -763.58
LRT: 1/2 * pchisq(73.3), p-val 5.67e-18
>
> # plot the Empirical Bayes estimates of the frailty
> # easy way:
> plot(mod_gamma, type = "hist")
>
> # a fancy graph:
> sum_mod <- summary(mod_gamma)
> 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(ggplot2)
>
> # Create a plot just with the points
> pl1 <- sum_mod$frail %>%
+ arrange(z) %>%
+ mutate(x = 1:n()) %>%
+ ggplot(aes(x = x, y = z)) +
+ geom_point()
>
> # If the quantiles of the posterior distribution are
> # known, then error bars can be added:
> if(!is.null(sum_mod$frail$lower_q))
+ pl1 <- pl1 + geom_errorbar(aes(ymin = lower_q, ymax = upper_q), alpha = 0.5)
>
> pl1
>
> # The plot can be made interactive!
> # ggplot2 gives a warning about the "id" aesthetic, just ignore it
> pl2 <- sum_mod$frail %>%
+ arrange(z) %>%
+ mutate(x = 1:n()) %>%
+ ggplot(aes(x = x, y = z)) +
+ geom_point(aes(id = id))
Warning in geom_point(aes(id = id)) : Ignoring unknown aesthetics: id
>
> if(!is.null(sum_mod$z$lower_q))
+ pl2 <- pl2 + geom_errorbar(aes(ymin = lower_q, ymax = upper_q, id = id), alpha = 0.5)
>
> library(plotly)
Attaching package: ‘plotly’
The following object is masked from ‘package:ggplot2’:
last_plot
The following object is masked from ‘package:stats’:
filter
The following object is masked from ‘package:graphics’:
layout
> ggplotly(pl2)
>
> # Proportional hazards test
> off_z <- log(sum_mod$frail$z)[match(bladder1$id, sum_mod$frail$id)]
>
> zph1 <- cox.zph(coxph(Surv(start, stop, status) ~ treatment + cluster(id), data = bladder1))
Warning in Surv(start, stop, status) :
Stop time must be > start time, NA created
Warning in Surv(start, stop, status) :
Invalid status value, converted to NA
Warning in Surv(start, stop, status) :
Stop time must be > start time, NA created
Warning in Surv(start, stop, status) :
Invalid status value, converted to NA
Error in a$specials[[i]] : subscript out of bounds
Calls: cox.zph ... model.matrix -> model.matrix.coxph -> delete.response -> off
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘frailtyEM_manual.Rnw’ using Sweave
Loading required package: survival
Loading required package: gridExtra
Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more
information.
ℹ The deprecated feature was likely used in the frailtyEM
package.
Please report the issue at
<https://github.com/tbalan/frailtyEM/issues>.
Warning: The `<scale>` argument of `guides()` cannot be `FALSE`. Use
"none" instead as of ggplot2 3.3.4.
Warning: Removed 2 rows containing missing values or values outside
the scale range (`geom_path()`).
Warning in data("kidney") : data set ‘kidney’ not found
Error: processing vignette 'frailtyEM_manual.Rnw' failed with diagnostics:
chunk 16 (label = kidneyb)
Error in a$specials[[i]] : subscript out of bounds
--- failed re-building ‘frailtyEM_manual.Rnw’
SUMMARY: processing the following file failed:
‘frailtyEM_manual.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc