[R] NLME model question

[Darren Shaw]

Dear R-helpers

I have a problem related to the use of NLME

I think is simply a matter of getting the nlme coding correct, but i cannot 
get my brain around it

I am analysing some 24 growth curves of some cells , and i wanted to say 
that there are significant differences between the curves in two parameters 
that describe the pattern of growth.  these parameters are from a logistic 
(r & k) .

i have attempted to construct a self starting routine for nlme ie:

SSGrowth_function(x, r, k)
{
         .expr2 <- (k - 100000)/100000
         .expr5 <- exp(((r * -1) * x))
         .expr7 <- 1 + (.expr2 * .expr5)
         .expr13 <- .expr7^2
         .value <- k/.expr7
         .actualArgs <- match.call()[c("r", "k")]
         if(all(unlist(lapply(as.list(.actualArgs), is.name)))) {
                 .grad <- array(0, c(length(.value), 2), list(NULL, c("r", 
"k")))
                 .grad[, "r"] <-  - ((k * (.expr2 * (.expr5 * (-1 * 
x))))/.expr13)
                 .grad[, "k"] <- (1/.expr7) - ((k * (1e-005 * .expr5))/.expr13)
                 dimnames(.grad) <- list(NULL, .actualArgs)
                 attr(.value, "gradient") <- .grad
         }
         .value
}

where x = time, 100000 = known starting conditions, r = growth and k = 
carrying capacity

  i guessed i should then write

nlme(NoofCells~SSGrowth(Time,r,k),fixed=r+k~1,data=CellData,random=r+k~1)


This runs and tells me that r & k's do differ

BUT.  The "CellData" actually consists of replicates - ie there are 4 cell 
types, but they are done 6 times each.  Therefore, I do not want to ask if 
there are significant differences in r & k between 24 sets of data 
("Runs")- rather I want to be able to say that there are differences 
between the four cell types occurring 6 times each.  So how do 
i  incorporate "CellType" explicitly into my model structure??

i.e. If i was lust looking at say linear growth and was using lme I would 
have written something like

lme(NoofCells~Time*CellType,random=~1|Runs,data=CellData)

Any thoughts/suggestions gratefully received

Darren Shaw

-----------------------------------------------------------------
Dr Darren J Shaw
Centre for Tropical Veterinary Medicine (CTVM)
Royal School of Veterinary Studies
The University of Edinburgh
Scotland