[R-sig-Geo] Faster way to get raster average?

[Kenny Bell]

You could also try out RRO with MKL
<http://mran.revolutionanalytics.com/download/#download>, which I have
found speeds up some basic computations on multicore machines.

On Tue, May 5, 2015 at 9:27 PM, Robert J. Hijmans <r.hijmans at gmail.com>
wrote:

> This suggest that most of the time is spend on reading data from disk.
> It could be more efficient to do this in one step.
>
> m <- .colMeans(getValues(cmip), nrow(cmip), ncol(cmip), na.rm=FALSE)
>
> I do not think there is much more you can do beyond that --- although
> a solid state hard disk could help.
>
> ( I am guessing that na.rm=FALSE is tiny bit faster, and that you do
> not need it to be TRUE. )
>
> Robert
>
> On Tue, May 5, 2015 at 6:48 PM, Thiago V. dos Santos
> <thi_veloso at yahoo.com.br> wrote:
> > Hi all,
> > I am working with some terabytes of CMIP5 climate files. Each file is a
> netcdf with multiple layers (timesteps) representing monthly data.
> > For each file, I need to extract the average value of the raster and put
> all values in a data frame. This is my current approach:---------------
> > library(raster)
> > # make up some datacmip <- brick(nc=150, nr=114, nl=1872)cmip <-
> setValues(cmip, matrix(rep(1:17100, 1872), nc=1872))
> > # get mean values (area average) as data framescmip.mean <-
> as.data.frame(cellStats(cmip, mean, na.rm=T))---------------
> > which works pretty fast in this example:
> >> system.time(as.data.frame(cellStats(cmip, mean, na.rm=T)))
> >    user  system elapsed
> >   0.069   0.012   0.081
> > However, the calculation with my actual data is substantially slower:
> >> system.time(as.data.frame(cellStats(cmip, mean, na.rm=T)))
> >    user  system elapsed
> >   4.600   1.105   5.704
> > Since I will have to deal with thousands of files, here comes my
> question: is there a faster way to get a the average value of a raster ?
> > Many thanks,
> > --
> > Thiago V. dos Santos
> > PhD student
> > Land and Atmospheric Science
> > University of Minnesota
> >
> http://www.laas.umn.edu/CurrentStudents/MeettheStudents/ThiagodosSantos/index.htm
> > Phone: (612) 323 9898
> >         [[alternative HTML version deleted]]
> >
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>
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-- 
Kendon Bell
Email: kmb56 at berkeley.edu
Phone: (510) 612-3375

Ph.D. Student
Department of Agricultural & Resource Economics
University of California, Berkeley

Graduate Student Researcher
Energy Biosciences Institute
http://www.energybiosciencesinstitute.org/

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