[R-sig-ME] Out of memory with spatial correlation.
d.rizopoulos at erasmusmc.nl
Tue Dec 9 15:13:35 CET 2008
Is it reasonable to assume that spatial correlation only exists within
lme(log(Pulses + 1) ~ Transport + Occasion, random = ~ 1 | Group,
correlation = corExp(form = ~ X + Y | Group))
ONKELINX, Thierry wrote:
> 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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