[R] NLME model question

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From: Darren Shaw (Darren.Shaw@ed.ac.uk)
Date: Fri 14 May 2004 - 20:11:07 EST

Message-id: <>

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",
                 .grad[, "r"] <- - ((k * (.expr2 * (.expr5 * (-1 *
                 .grad[, "k"] <- (1/.expr7) - ((k * (1e-005 * .expr5))/.expr13)
                 dimnames(.grad) <- list(NULL, .actualArgs)
                 attr(.value, "gradient") <- .grad

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

  i guessed i should then write


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


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

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