collett

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: step_s
> ### Title: Utilities
> ### Aliases: step_s as.data.frame.survfit as.data.frame.summary.survfit
> ###   predict_coxph_tt predict_coxph_tv plot_coxph_functional
> 
> ### ** Examples
> 
>   step_s(data.frame(g=c(1,1), a=1:2, b=4:5), a, b)
  g a b
1 1 0 1
2 1 1 1
3 1 1 4
4 1 2 4
5 1 2 5
>   step_s(data.frame(g=c(2,2), a=3:4, b=6:7), a, b)
  g a b
1 2 0 1
2 2 3 1
3 2 3 6
4 2 4 6
5 2 4 7
>   step_s(data.frame(g=c(1,1,2,2), a=1:4, b=4:7), a, b, group=g)
   g a b
1  1 0 1
2  1 1 1
3  1 1 4
4  1 2 4
5  1 2 5
6  2 0 1
7  2 3 1
8  2 3 6
9  2 4 6
10 2 4 7
>   library(survival)

Attaching package: ‘survival’

The following objects are masked from ‘package:collett’:

    bladder, kidney, lung, myeloma, ovarian

>   library(tinyplot)
>   sfit1 = survfit(Surv(time,status)~rx, data=survival::colon,
+                   subset=etype==1)
>   with(as.d
...[truncated]...

+                  model="ns",times=times)
>  with(rbind(df1,df2),
+       plt(fitted ~ times | model, ymin=lower, ymax=upper, type="ribbon",
+           xlab="Time since diagnosis (days)",
+           ylab="Hazard ratio comparing treated with untreated"))
>  with(subset(breast_rfs,status==1), rug(time))
> library(survival)
> liver = transform(collett::liverbase, lbr=NULL)
> liver = tmerge(liver, liver, id=patient, status=event(time,status))
> liver = tmerge(liver,
+                rbind(with(collett::liverbase, data.frame(patient,tstart=0,lbr)),
+                      with(collett::lbrdata0, data.frame(patient,tstart=time,lbr))),
+            id=patient, lbr = tdc(tstart,lbr))
> fit3 = coxph(Surv(tstart,tstop,status)~lbr+treat,liver)
> predict_coxph_tv(fit3,data=subset(liver,patient %in% c(1,7)),
+                  id="patient")
Error in a$specials[[i]] : subscript out of bounds
Calls: predict_coxph_tv ... survfit.coxph -> model.matrix.coxph -> delete.response -> off
Execution halted