-----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 ONKELINX, Thierry
Sent: Tuesday, December 09, 2008 7:59 AM
To: R-sig-mixed-models at r-project.org
Subject: [R-sig-ME] Out of memory with spatial correlation.
Dear all,
My model runs fine with just the fixed and random effects.
But when I add a spatial correlation structure it runs out of
memory (Error: cannot allocate vector of size 185.6 Mb). The
problem is that the data is clearly spatially correlated. I
have tried the simplify the fixed effects and the random
effects with no avail. So the problem is probably in the
correlation structure (see code below). Any suggestion on how
to incorporate the spatial autocorrelation?
A description of the design.
We are testing a methodology to monitor bats. Basically
volunteers ride along a predefined route by car (30 km/h) or
by bike (15 km/h). They record the echolocation sounds of the
bats at fixed intervals. There position is tracked by GPS so
we know were each recording was made. An expert counts the
number of pulses in each recording.
We predefined 10 routes, 5 for the cars and 5 for the bikes.
Each car route overlaps with one bike route. So we have 5
groups of routes.
Within each group we have an longer car route that overlaps
with a shorter bike route. There is no overlap between
groups. All routes were driven three times, all vehicules
started their route simultanious.
We have about 400 recordings per route of 10 routes at 3
occasions = 12000 rows.
Our nullhypothese is that the average number of recordings
does not depend on the type of vehicule.
The model that fails is:
library(nlme)
lme(log(Pulses + 1) ~ Transport + Occasion, random = ~ 1|
Group, correlation = corExp(form = ~ X + Y))
The model works if I omit the correlation structure:
lme(log(Pulses + 1) ~ Transport + Occasion, random = ~ 1| Group)
I'm using R 2.8.0 with nlme 3.1-89 on WinXP with 2GB RAM.
--mem-size is set at the maximum (2047 MB).
Regards,
Thierry
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ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute
for Nature and Forest Cel biometrie, methodologie en
kwaliteitszorg / Section biometrics, methodology and quality
assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32
54/436 185 Thierry.Onkelinx at inbo.be www.inbo.be
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~ Sir Ronald Aylmer Fisher
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