From: Stephen <szlevine_at_nana.co.il>

Date: Mon 27 Jun 2005 - 15:40:02 EST

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Mon Jun 27 15:48:30 2005

Date: Mon 27 Jun 2005 - 15:40:02 EST

Hi

Thank you for your comments.

Yes you are correct its a very big data set.
Perhaps I am best splitting it up and then importing to R.
The reason for the loop is that I am conducting the equivalent of Split
file in SPSS.

Specifically, I am conducting the analysis for each value of on the
grouping variable 'runnb'.

If there is a less memory intensive way of doing this I'd appreciate
knowing about it.

Many Thanks and comments appreciated

Regards

Stephen

From: Douglas Bates [mailto:dmbates@gmail.com]
Sent: Sun 26/06/2005 17:01

To: Stephen

Cc: r-help@stat.math.ethz.ch

Subject: Re: [R] Mixed model

On 6/26/05, Stephen <szlevine@nana.co.il> wrote:

*>
**>
**>
*

> Hi All,

*>
**>
**>
**> I am currently conducting a mixed model. I have 7 repeated measures on
*

a

> simulated clinical trial. If I understand the model correctly, the

*> outcome is the measure (as a factor) the predictors are clinical group
**> and trial (1-7). The fixed factors are the measure and group. The
*

random

> factors are the intercept and id and group.

*>
**>
**>
**> I tried using 2 functions to calculate mixed effects.
**>
**> Following previous correspondence .
**>
**>
**>
**> Dataset <- read.table("C:/Program
*

Files/R/rw2011/data/miss/model1a.dat",

> header=TRUE, sep="\t", na.strings="NA", dec=".", strip.white=TRUE)

*>
**> attach(Dataset)
**>
**>
**>
**> require (nlme)
**>
**> with(Dataset, table(runnb, id, grp))
**>
**> b.lvls <- table(Dataset$runnb)
**>
**> nb <- length(b.lvls)
**>
**> fit <- vector(mode="list", nb)
**>
**>
**>
**> for(i in 1:nb)
**>
**> fit[[i]]<- lme (trans1 ~ Index1 + grp,
**>
**> random = ~ 1 | id / grp ,
**>
**> data = Dataset,
**>
**> na.action = "na.exclude")
**>
**>
**>
**>
**>
**> This (above) worked OK only I am having memory problems.
**>
**> I have a gig of RAM set at --sdi --max-mem-size=512M (complete version
**> below)
**>
**> I am wondering if running the file as a database be slower / faster?
**>
**>
**>
**> Then I read that lme4 does it quicker and more accurately
**>
**> so I thought that I should re-run the code but from the for line:
**>
**>
**>
**> > for (i in 1:nb)
**>
**> + fit[[i]] <- lmer(trans1 ~ Index1 + grp + (1|id:grp) + (1|id),
**>
**> + Dataset, na.action = na.exclude)
**>
**>
**>
**> Producing
**>
**>
**>
**> Error in lmer(trans1 ~ Index1 + grp + (1 | id:grp) + (1 | id),
*

Dataset,

*> :
**>
*

> flist[[2]] must be a factor of length 200000

*>
**> In addition: Warning messages:
**>
**> 1: numerical expression has 200000 elements: only the first used in:
**> id:grp
**>
**> 2: numerical expression has 200000 elements: only the first used in:
**> id:grp
*

Check

str(Dataset)

and, if necessary, convert id to a factor with

Dataset$id <- factor(Dataset$id)

In is not surprising that you are running into memory problems. Look at the size of one of the fitted objects from lme or from lmer. They are very large because they contain a copy of the model frame (the parts of Dataset that are needed to evaluate the model) plus a lot of other information. You have a large Dataset and you are saving multiple copies of it although I must admit that I don't understand why the calls to lme or lmer are in a loop.

???? ?"? ???? ????

http://mail.nana.co.il

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R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Mon Jun 27 15:48:30 2005

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