Running examples in ‘tram-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: perm_test
> ### Title: Permutation Transformation Tests
> ### Aliases: perm_test perm_test.tram
> 
> ### ** Examples
> 
> 
>   ## Tritiated Water Diffusion Across Human Chorioamnion
>   ## Hollander and Wolfe (1999, p. 110, Tab. 4.1)
>   diffusion <- data.frame(
+       pd = c(0.80, 0.83, 1.89, 1.04, 1.45, 1.38, 1.91, 1.64, 0.73, 1.46,
+              1.15, 0.88, 0.90, 0.74, 1.21),
+       age = factor(rep(c("At term", "12-26 Weeks"), c(10, 5)))
+   )
> 
>   ### plot the two quantile functions
>   boxplot(pd ~ age, data = diffusion)
> 
>   ### the Wilcoxon rank sum test, with a confidence interval
>   ### for a median shift
>   wilcox.test(pd ~ age, data = diffusion, conf.int = TRUE, exact = TRUE)

	Wilcoxon rank sum exact test

data:  pd by age
W = 15, p-value = 0.2544
alternative hypothesis: true location shift is not equal to 0
95 percent confidence interval:
 -0.76  0.15
sample estimates:
difference in location 
                -0.305 

> 
>   ### a corresponding parametric transformation model with a log-odds ratio
>   ### difference parameter, ie a difference on the log-odds scale
>   md <- Colr(pd ~ age, data = diffusion)
> 
>   ### assess model fit by plotting estimated distribution fcts
>   agef <- sort(unique(diffusion$age))
>   col <- c("black", "darkred")
>   plot(as.mlt(md), newdata = data.frame(age = agef),
+        type = "distribution", col = col)
>   legend("bottomright", col = col, lty = 1, legend = levels(agef), 
+          bty = "n", pch = 19)
>   ## compare with ECDFs: not too bad (but not good, either)
>   npfit <- with(diffusion, tapply(pd, age, ecdf))
>   lines(npfit[[1]], col = col[1])
>   lines(npfit[[2]], col = col[2])
> 
>   ### Wald confidence interval
>   confint(md)
               2.5 %   97.5 %
ageAt term -3.346447 0.549622
> 
>   ### Likelihood confidence interval
>   confint(profile(md))
     2.5 %     97.5 % 
-3.4432762  0.4982587 
> 
>   ### Score confidence interval
>   confint(score_test(md))
               2.5 %    97.5 %
ageAt term -3.268074 0.4791056
>   confint(score_test(md, Taylor = TRUE))
Warning in score_test.tram(md, Taylor = TRUE) :
  cannot compute score interval, returning Wald interval
               2.5 %   97.5 %
ageAt term -3.346447 0.549622
> 
>   ### exact permutation score test
>   (pt <- perm_test(md, confint = TRUE, distribution = "exact"))
Error in loadNamespace(x) : there is no package called ‘coin’
Calls: perm_test ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
mmlt  4.255  0.067   5.544
Coxph 4.070  0.008   5.726
mtram 3.641  0.081   5.041