Last updated on 2025-12-07 07:50:29 CET.
| Package | ERROR | NOTE |
|---|---|---|
| frailtyEM | 1 | 12 |
Current CRAN status: ERROR: 1, NOTE: 12
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)
Error in library(plotly) : there is no package called ‘plotly’
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.1
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64