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

[ONKELINX, Thierry]

Dear Dimitris,

Restricting the correlation to the Group (and to Occasion nested in
Group) did not solve my problem. I even tried to subset the data to one
groep with no avail.

Regards,

Thierry 


------------------------------------------------------------------------
----
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 

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey

-----Oorspronkelijk bericht-----
Van: Dimitris Rizopoulos [mailto:d.rizopoulos at erasmusmc.nl] 
Verzonden: dinsdag 9 december 2008 15:14
Aan: ONKELINX, Thierry
CC: R-sig-mixed-models at r-project.org
Onderwerp: Re: [R-sig-ME] Out of memory with spatial correlation.

Is it reasonable to assume that spatial correlation only exists within 
groups, e.g.,

lme(log(Pulses + 1) ~ Transport + Occasion, random = ~ 1 | Group, 
correlation = corExp(form = ~ X + Y | Group))


Best,
Dimitris


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:
> 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
> 
> 
>
------------------------------------------------------------------------
> ----
> 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 
> 
> To call in the statistician after the experiment is done may be no
more
> than asking him to perform a post-mortem examination: he may be able
to
> say what the experiment died of.
> ~ Sir Ronald Aylmer Fisher
> 
> The plural of anecdote is not data.
> ~ Roger Brinner
> 
> The combination of some data and an aching desire for an answer does
not
> ensure that a reasonable answer can be extracted from a given body of
> data.
> ~ John Tukey
> 
> Dit bericht en eventuele bijlagen geven enkel de visie van de
schrijver weer 
> en binden het INBO onder geen enkel beding, zolang dit bericht niet
bevestigd is
> door een geldig ondertekend document. The views expressed in  this
message 
> and any annex are purely those of the writer and may not be regarded
as stating 
> an official position of INBO, as long as the message is not confirmed
by a duly 
> signed document.
> 
> _______________________________________________
> R-sig-mixed-models at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> 

-- 
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus Medical Center

Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
Tel: +31/(0)10/7043478
Fax: +31/(0)10/7043014


Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer 
en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is
door een geldig ondertekend document. The views expressed in  this message 
and any annex are purely those of the writer and may not be regarded as stating 
an official position of INBO, as long as the message is not confirmed by a duly 
signed document.