**From:** Douglas Bates (*bates@stat.wisc.edu*)

**Date:** Fri 14 May 2004 - 21:49:43 EST

**Next message:**javier garcia - CEBAS: "[R] integrate over a serie"**Previous message:**Murray Jorgensen: "Re: [R] Problem with logtrans, from library MASS"**In reply to:**Darren Shaw: "[R] NLME model question"**Next in thread:**kjetil@acelerate.com: "Re: [R] NLME model question"

Message-id: <6r7jvfut2g.fsf@bates4.stat.wisc.edu>

Darren Shaw <Darren.Shaw@ed.ac.uk> writes:

*> 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
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*> say that there are significant differences between the curves in two
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*> parameters that describe the pattern of growth. these parameters are
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*> from a logistic (r & k) .
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*>
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*>
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*> i have attempted to construct a self starting routine for nlme ie:
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*>
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*> SSGrowth_function(x, r, k)
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*> {
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*> .expr2 <- (k - 100000)/100000
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*> .expr5 <- exp(((r * -1) * x))
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*> .expr7 <- 1 + (.expr2 * .expr5)
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*> .expr13 <- .expr7^2
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*> .value <- k/.expr7
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*> .actualArgs <- match.call()[c("r", "k")]
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*> if(all(unlist(lapply(as.list(.actualArgs), is.name)))) {
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*> .grad <- array(0, c(length(.value), 2), list(NULL,
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*> c("r", "k")))
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*>
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*> .grad[, "r"] <- - ((k * (.expr2 * (.expr5 * (-1 *
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*> x))))/.expr13)
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*>
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*> .grad[, "k"] <- (1/.expr7) - ((k * (1e-005 * .expr5))/.expr13)
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*> dimnames(.grad) <- list(NULL, .actualArgs)
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*> attr(.value, "gradient") <- .grad
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*> }
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*> .value
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*> }
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*>
*

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

*> i guessed i should then write
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*>
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*> nlme(NoofCells~SSGrowth(Time,r,k),fixed=r+k~1,data=CellData,random=r+k~1)
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*>
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*>
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*> This runs and tells me that r & k's do differ
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*>
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*> BUT. The "CellData" actually consists of replicates - ie there are 4
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*> cell types, but they are done 6 times each. Therefore, I do not want
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*> to ask if there are significant differences in r & k between 24 sets
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*> of data ("Runs")- rather I want to be able to say that there are
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*> differences between the four cell types occurring 6 times each. So
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*> how do i incorporate "CellType" explicitly into my model structure??
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*>
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*>
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*> i.e. If i was lust looking at say linear growth and was using lme I
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*> would have written something like
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*>
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*>
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*> lme(NoofCells~Time*CellType,random=~1|Runs,data=CellData)
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*>
*

*> Any thoughts/suggestions gratefully received
*

I believe you want

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

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**Next message:**javier garcia - CEBAS: "[R] integrate over a serie"**Previous message:**Murray Jorgensen: "Re: [R] Problem with logtrans, from library MASS"**In reply to:**Darren Shaw: "[R] NLME model question"**Next in thread:**kjetil@acelerate.com: "Re: [R] NLME model question"

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