[R-sig-ME] glmmADMB v 0.7.1

[Chris Howden]

Hi Chris,

If it's getting upto 2GB that's about the limit on your machine unless U
manually change it (see ?memory-limit for more info)

Have u tried removing all unnecessary objects from the workspace and then
garbage collecting: gc()?

The following code may help:

# Set Memory parameters
# Help on memory limits
?Memory-limits
# Remove unneccessary objects (in this call everything)
rm(list=ls())
ls()
# Garbage collection, this can increase available memory after a call to
rm()
gc()
# Set Memory Limit to Max on a 4GB machine
memory.limit(size=4095)
# report memory limit
memory.limit(size=NA)
# maximum amount of memory obtained from the OS is reported
memory.limit(size=TRUE)
# amount currently in use
memory.limit(size=FALSE)

Chris Howden B.Sc. (Hons) GStat.
Founding Partner
Evidence Based Strategic Development, IP Commercialisation and Innovation,
Data Analysis, Modelling and Training
(mobile) 0410 689 945
(fax) +612 4782 9023
chris at trickysolutions.com.au




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-----Original Message-----
From: r-sig-mixed-models-bounces at r-project.org
[mailto:r-sig-mixed-models-bounces at r-project.org] On Behalf Of Christopher
Rota
Sent: Friday, 13 January 2012 4:27 AM
To: r-sig-mixed-models at r-project.org
Subject: [R-sig-ME] glmmADMB v 0.7.1

Dear R Users,

I am running into some trouble when using glmmADMB version 0.7.1 and am
hoping someone in the R community may have some insight.

I am trying to fit a rather large negative binomial mixed-effects
model.  I have 3980 observations (counts of foraging attempts).  My
'global' model has 17 fixed effects and 2 random effects.  Fixed effects
consist of both continuous and categorical variables.  Each categorical
variable has at least 22 observations, most have considerably more.  One
random effect is an 'observer' effect consisting of 11 different
observers.  Each observer made at least 29 observations, but most made
considerably more.  The other random effect in an 'individual bird'
effect consisting of 78 individual birds.  There are at least 20
observations made on each bird.

Here is my call to glmmadmb:
fit <- glmmadmb(formula=count~BrnLight + BrnMod + BrnMPB + BrnSev +
GrnHit + GryHit + RedHit + Autumn + Spring + Winter + Yr01 + Yr12 + Yr23
+ Yr34 + Yr45 + Est.DBH.in + Start.Time + (1|Color.Combo) +
(1|Observers), data=beh.data, family='nbinom')

The variables 'BrnLight' through 'RedHit' represent categorical
variables describing tree condition.  They are coded as dummy variables,
and one tree condition category (Green) is omitted from model
specification and interpreted as the intercept.  The season (Autumn,
Spring, Winter) and year (Yr01, etc.) variables are coded in an
identical manner (note that I also coded categorical variables as
factors, and encountered the same problem described below).  DBH and
Start.Time are continuous variables.

This global model runs for about 10 minutes, then fails with the
following message:
Memory allocation error -- Perhaps you are trying to allocate too much
memory in your program

When I monitor my computer performance with Windows Task Manager while
the model is running, I can watch Physical Memory Usage slowly tick up.
All of that increased memory use is attributed to glmmadmb.exe.  I will
watch memory use for this program tick up to about 1.7GB, and that is
when the model fails.  I am using a computer with a Windows Vista 32-bit
operating system with 4GB RAM.  Is the problem simply that I do not have
enough memory on my computer to run this model?  If indeed the problem
is a shortage of memory, is there any way to make glmmadmb.exe use
memory differently, or do I need to use a more powerful computer?

Thank you for any insight.

Chris Rota

--
Christopher Rota
Ph.D. Student

University of Missouri
Fisheries and Wildlife Science
302 Anheuser-Busch Natural Resources Building
Columbia, MO 65211

Office:  303O Anheuser-Busch Natural Resources Buildling
Email:  ctr4g2 at mail.missouri.edu
Phone:  573-239-6975
Website:  http://www.biosci.missouri.edu/avianecology/rota/index.html
Calendar:
http://www.google.com/calendar/embed?src=christopher.rota%40gmail.com&ctz=
America/Chicago

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