[R] coxme - fitting random treatment effect nested within centre

[Terry Therneau]

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 Dear all,

I am using "coxme" function in Kinship library to fit random treatment effect 
nested within centre. I got 3 treatments (0,1,2) and 3 centres. I used following 
commands, but got an error. 

> ugroup=paste(rep(1:3,each=3),rep(0:2,3),sep='/')
> 
mat1=bdsmatrix(rep(c(1,1,1,1,1,1,1,1,1),3),blocksize=rep(3,3),dimnames=list(ugro
up,ugroup))
> 
mat2=bdsmatrix(rep(c(0,0,0,0,0,0,0,0,1),3),blocksize=rep(3,3),dimnames=list(ugro
up,ugroup))
> group=paste(dat1$centre,dat1$treat,sep='/')
> coxme(Surv(time,status) ~ as.factor(treat), data=dat1,random= 
~1|group,varlist=list(mat1,mat2),rescale=F,pdcheck=FALSE)

Error in coxme.fit(X, Y, strats, offset, init, control, weights = weights, : 
Random effects variance is not spd
 
Could anyone help me correcting this error? 
Many thanks in advance.
Ruwanthi

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 The "build your own bdsmatrix" style in coxme is for variance structures that 
are not built in, like pedigree data.  Your problem is one that coxme can do 
directly, so it is easier to call the routine simply:
 
  fit <- coxme(Surv(time, status) ~ factor(treat), data=data1,
  	         random = ~1 | centre/treat)
  	       
	Terry Therneau