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

[Rainer M Krug]

"Thiago V. dos Santos" <thi_veloso at yahoo.com.br> writes:

> Oh, I forgot to mention that I work on a quad-core Mac with 12GB.

> So, if multi-core can potentially accelerate cellStats, or whatever
> function is faster to get a raster average, I would be glad to see
> some examples on how to implement it. Greetings,

The key question is: how often do you have to do the calculations and if
it would be feasible to just let them run for a few days and be done
with it - optimization takes time!

Cheers,

Rainer

> --
> 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 
>
>
>      On Tuesday, May 5, 2015 8:48 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
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>
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-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
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Fax :       +33 - (0)9 58 10 27 44

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email:      Rainer at krugs.de

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