Re: [R] NLME model question

About this list Date view Thread view Subject view Author view Attachment view

From: Douglas Bates (bates@stat.wisc.edu)
Date: Fri 14 May 2004 - 21:49:43 EST


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
> 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

I believe you want

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

______________________________________________
R-help@stat.math.ethz.ch mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html


About this list Date view Thread view Subject view Author view Attachment view

This archive was generated by hypermail 2.1.3 : Mon 31 May 2004 - 23:05:10 EST