[R-sig-eco] memory issues using Tps (package fields)

[Jorge Velasquez]

Dear Robert,

Thanks a lot for your help...it worked! It's very impressive that the
interpolate funcion can process almost 2 million cells in less than 10
minutes.

Jorge

On Fri, Jun 18, 2010 at 12:30 AM, Robert J. Hijmans <r.hijmans at gmail.com> wrote:
> Hi Jorge,
>
> I might work if you specify "dem" as an independent variable rather
> than as a co-variable (z). (If you really want it to be a co-variable
> it would take a bit of tweaking of the interpolate function). You also
> need to add "xyOnly = F" to predict (not obvious from docs).
>
> data<-read.table("precp00-09ContSampleDem.csv", sep="," , header=TRUE)
> fit<-Tps( data[ , c("x","y", "dem") ],  data[,"Ene"] )
> elev=raster("dem_col.asc")
> result<-interpolate(elev, fit, xyOnly=FALSE)
>
> (I cannot test this as I do not have (a sample of) your data)
>
> Robert
>
> On Thu, Jun 17, 2010 at 8:33 PM, Jorge Velasquez
> <jorge at life.bio.sunysb.edu> wrote:
>> Hi Robert,
>>
>> I tried the solution you suggested but get the following error:
>>
>> Error in predict.Krig(model, blockvals, ...) :
>>  Need to specifify drop.Z as TRUE or pass Z values
>>
>> This is the code I used:
>>
>> data<-read.table("precp00-09ContSampleDem.csv",sep=",",header=TRUE)
>> fit<-Tps(data[,c("x","y")],data[,"Ene"],z=data$dem)
>> elev=raster("dem_col.asc")
>> result<-interpolate(elev,fit)
>>
>> Many thanks indeed for your reply,
>>
>> Jorge
>>
>> On Thu, Jun 17, 2010 at 3:49 PM, Robert J. Hijmans <r.hijmans at gmail.com> wrote:
>>> Jorge,
>>> You could use the function 'interpolate' in 'raster'. It makes
>>> predictions for smaller chunks of data and puts these back together.
>>> There is an example for Tps. You would need to provide elevation data
>>> (as a RasterLayer) as the first argument.
>>> Robert
>>>
>>> On Thu, Jun 17, 2010 at 1:25 PM, Jorge Velasquez
>>> <jorge at life.bio.sunysb.edu> wrote:
>>>> Hi there,
>>>>
>>>> I'm trying to run a interpolation of climate using the functionTps
>>>> (Thin plated splines) from the package fields, but keep running into
>>>> the following error:
>>>>
>>>> Error: cannot allocate vector of size 488 Kb
>>>> In addition: Warning messages:
>>>> 1: In names(y) <- make.unique(cols) :
>>>>  Reached total allocation of 3583Mb: see help(memory.size)
>>>> 2: In names(y) <- make.unique(cols) :
>>>>  Reached total allocation of 3583Mb: see help(memory.size)
>>>> 3: In names(y) <- make.unique(cols) :
>>>>  Reached total allocation of 3583Mb: see help(memory.size)
>>>> 4: In names(y) <- make.unique(cols) :
>>>>  Reached total allocation of 3583Mb: see help(memory.size)
>>>> Error in as.matrix(expand.grid(grid.list)) :
>>>>  error in evaluating the argument 'x' in selecting a method for
>>>> function 'as.matrix'
>>>>
>>>> The code I'm running is:
>>>>
>>>> predGrid<-read.table("demaspoint_id8.csv" ,sep="," ,header=TRUE)
>>>> data<-read.table("precp00-09ContSampleDem.csv",sep="," ,header=TRUE)
>>>> fit<-Tps(data[,c("x","y")],data[,"Ene"],Z=data$dem)
>>>> result<-predict.surface(fit,grid.list=list(x=predGrid[,c("Longitude","Latitude")],Z=predGrid[,"GRID_CODE"]))
>>>>
>>>> The file predGrid has ~65000 rows. The error is persistent even using
>>>> a machine with 8GB Ram, double xeon processor, and the 64bit version
>>>> of R, although the error pasted above is for the 32 bit version.
>>>>
>>>> Is there any solution to this? Am I missing something?
>>>>
>>>> Thanks,
>>>>
>>>> Jorge
>>>> --
>>>> ---
>>>> Jorge Velasquez
>>>> Department of Ecology and Evolution
>>>> Stony Brook University
>>>> Stony Brook, NY 11974
>>>> Phone:(631) 632-1445
>>>> http://life.bio.sunysb.edu/~jorge/
>>>>
>>>> _______________________________________________
>>>> R-sig-ecology mailing list
>>>> R-sig-ecology at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>>>
>>>
>>>
>>
>>
>>
>> --
>> ---
>> Jorge Velasquez
>> Department of Ecology and Evolution
>> Stony Brook University
>> Stony Brook, NY 11974
>> Phone:(631) 632-1445
>> http://life.bio.sunysb.edu/~jorge/
>>
>
>



-- 
---
Jorge Velasquez
Department of Ecology and Evolution
Stony Brook University
Stony Brook, NY 11974
Phone:(631) 632-1445
http://life.bio.sunysb.edu/~jorge/