[R-sig-ME] Out of memory with spatial correlation.

ONKELINX, Thierry Thierry.ONKELINX at inbo.be
Tue Dec 9 13:59:18 CET 2008

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:
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).



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
tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be 

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