start values for random effects in nlme

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start values for random effects in nlme

Jos Lommerse
Hi Lindsey,

Yeah, I do realize that this answer gets to you 12 years too late, however, it may be helpful to others in future.
I have been struggling with the same issue. When analysing the source code (https://svn.r-project.org/R-packages/trunk/nlme/R/nlme.R)
I found out that the E matrix needs rownames referring to the random effect of each group in the dataset, something like:
rownames(E) <- c("subjectname1","subjectname2","subjectname3",.....).
Then your code should run perfectly OK.

Example:
----------
library(nlme)

data <- data.frame(a=c(1,2,3,4,5,1,2,3,4,5,1,2,3,4,5),
                   b=c(2,3,4,5,7,3,4,5,7,8,3,5,6,8,9),
                   ID=c(rep('X',5),rep('Y',5),rep('Z',5)))

# Random effect matrix E:
E <- as.matrix(c(-0.1,0.2,0.3))
rownames(E) <- c('X','Y','Z')
fm1 <- nlme(b ~ par1*a + par2*exp(IIV),
            data = data,
            fixed = list(par1 ~ 1, par2 ~ 1),
            random = IIV ~ 1 | ID,
            start = list(fixed = c(1,1), random= E))
summary(fm1)
---------

Kind regards,
Jos Lommerse, Certara


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