[R] Memory shortage running Repeated Measures (nlme)

From: Evandro do Nascimento Silva <evandro_at_uefs.br>
Date: Wed 14 Dec 2005 - 14:22:49 EST

Dear group,

I tried to run a Repeated Mesures Anova for Mixed effects model and I got a warnning after entering the model specification saying: "Reached total allocation of 254Mb: see help(memory.size)".

here is part of the log:



> aphids<-read.table("aphid.txt",header=T)
> attach(aphids)
> names(aphids)

[1] "site" "time" "shade" "treatp" "aphid"
> library(nlme)
> aphids<-groupedData(aphid~time|site/shade/treatp,data=aphids,outer=~shade*treatp)
> model<-lme(aphid~shade*treatp,random=~time|site)
Error in logLik.lmeStructInt(lmeSt, lmePars) :

        Calloc could not allocate (89359209 of 8) memory In addition: Warning message:
Reached total allocation of 254Mb: see help(memory.size)


My response variable is number of aphids/colony on shaded cocoa trees, measured over 15 days (which I treat as a random factor) in four sites (random factor), two levels of shade (fixed) within each site, and three aphid predation treatmens (fixed) within each shade level. My total N = 2,256 observations (actually counts).

The comand lines were the same as in the example in:

Crawley, M. J. 2002. Statistical Computing: an intro to data analysis using S-Plus. Wiley. pages: 702-704.

My questions are:

1-Did I use the appropriate analysis to my data?
2-Is the lack of memory caused by my large N and many factor interactions?
3-Since I have counts, should I specify (family=poisson) in the model? If
so, where in the command line this term must be located?

I am a complete beginner with R, so any help will be wellcome.

Evandro Silva
Assistant Professor
Universidade Estadual de Feira de Santana Laboratory of Insect Ecology
Feira de Santana, BA, Brazil



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