Re: [R] Mixed model

From: Stephen <szlevine_at_nana.co.il>
Date: Tue 28 Jun 2005 - 19:41:15 EST


Hi,  

Your last email was excellent and I got it working using the following.  

It did the job extremely quickly, more so a commercial piece of software my university uses!  

#This works fine -

Dataset <- read.table("C:/Program Files/R/rw2011/data/miss/model1.dat", header=TRUE, sep="\t", na.strings="NA", dec=".",strip.white=TRUE)

Dataset$id <- factor(Dataset$id)

attach(Dataset)

names (Dataset)

require (nlme)

fit <- vector(mode="list", 100)

i = 0  

for (i in 1:100)

{ Dataset2 <- subset(Dataset, subset= i == runnb)

       summary (fit[[i]]<- lme (trans1 ~ Index1 + grp,

               random = ~ 1 | id / grp ,

              data = Dataset2,

            na.action = "na.exclude")

            )

        i =i +1

}  

Strangely enough I was less lucky with LMER.

> for (i in 1:100)

+ { Dataset2 <- subset(Dataset, subset= i == runnb)

+ fit[[i]] <- lmer(trans1 ~ Index1 + grp + (1|id:grp) + (1|id), Dataset2, na.action = na.exclude)

+ i =i +1

+ }

Error in lmer(trans1 ~ Index1 + grp + (1 | id:grp) + (1 | id), Dataset2, :

        flist[[2]] must be a factor of length 4000

In addition: Warning messages:

  1. numerical expression has 4000 elements: only the first used in: id:grp
  2. numerical expression has 4000 elements: only the first used in: id:grp

>  

Many thanks to you all for your assistance on this issue.  

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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