Error in frailtypack

[Reza88]

When I enter continuous variables in the joint frailty model(function: frailtyPenal). I get the below error. however no error with factor variables.

Problem in the loglikelihood computation. The program stopped abnormally. Please verify your dataset.

Confused. anyone has same issue?

[jrkrideau]

We need a reproducible example (reprex)

FAQ: How to do a minimal reproducible example ( reprex ) for beginners

A minimal reproducible example consists of the following items: A minimal dataset, necessary to reproduce the issue The minimal runnable code necessary to reproduce the issue, which can be run on the given dataset, and including the necessary information on the used packages. Let's quickly go over each one of these with examples: Minimal Dataset (Sample Data) You need to provide a data frame that is small enough to be (reasonably) pasted on a post, but big enough to reproduce your issue. Let's say, as an example, that you are working with the iris data frame head(iris) #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.…

[Reza88]

My code

model<-frailtyPenal(Surv(time, event1) ~ cluster(ID) + age +
terminal(allcausedeath), formula.terminalEvent = ~ age,
data = All, n.knots = 6, kappa = c(100,100))

head(All$age)
[1] 59 57 67 56 84 84

head( All$time)
[1] 1611 1610 1376 1609 337 99

head(All$event1)
[1] 0 0 1 0 1 1

head(All$allcausedeath)
[1] 0 0 0 0 1 1

[jrkrideau]

To repeat

@jrkrideau

We need a reproducible example (reprex)

Data and code.

[Reza88]

library(survival)
library(frailtypack)
#> Loading required package: boot
#>
#> Attaching package: 'boot'
#> The following object is masked from 'package:survival':
#>
#> aml
#> Loading required package: MASS
#> Loading required package: survC1
#> Loading required package: doBy
#>
#> Attaching package: 'frailtypack'
#> The following object is masked from 'package:survival':
#>
#> cluster

time<-c(33,42,45,0.02,0.47,3,31,58,28,14,58,0.03,59,10,58,47,21,3,3,10,12,13,45,35,26,0.33,0.05,0.83,1,2)
status<-c(0,0,0,1,1,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0)
age<-c(20,20,22,20,18,17,21,20,20,26,29,24,30,32,28,24,20,22,26,24,21,29,29,32,17,32,35,19,25,24)
No.childrn_under5<-c(3,3,2,2,1,1,0,1,1,1,2,2,1,4,0,0,2,2,0,1,1,2,2,3,3,1,1,1,2,0)
source<-c("Piped water","Piped water","Piped water","Piped water","Piped water","well water","well water","Piped water",
"Piped water","Bottled water","Other","Surfaced water", "Piped water","Piped water","Piped water","Piped water",
"Piped water","Piped water","Piped water","Other","Other","Other","Other","Bottled water","Bottled water","Bottled water"
,"well water","well water","well water","Piped water")
hhId<-c(1,1,1,2,2,2,2,3,3,3,4,4,5,5,6,6,6,6,7,7,7,8,8,9,9,10,10,10,11,11)

data<-data.frame(time,status,age,No.childrn_under5,source,hhId)

######### CONVRTING CHARACTOR VARIABLES TO FACTOR VARIABLES
data <- data.frame(data, stringsAsFactors=FALSE)
data<- as.data.frame(unclass(data))

#shared frailty model
shared_frailty<-frailtyPenal(Surv(time,status)~cluster(hhId)+No.childrn_under5+age+source,
n.knots = 10,data=data, kappa=1000, cross.validation = TRUE,hazard = "Splines")
#>
#> Be patient. The program is computing ...
#> Warning in frailtyPenal(Surv(time, status) ~ cluster(hhId) + No.childrn_under5 + : Problem in the loglikelihood computation. The program stopped abnormally. Please verify your dataset.
The program took 0.06 seconds