[R-sig-Geo] polygonValues (raster): Very slow

[Robert J. Hijmans]

Dear Agus,

You are extracting values for 18000 polygons for a high res raster.
That is going to take a while. And using "weights=TRUE" is also bad
(in terms of processing speed!); do you really need it?. You can do
some testing by subsetting the polygons object.

If the polygons are not overlapping, you could consider to do
polygonsToRaster and then zonal. That would likely be much faster (but
you would not have the weights).

I have not attempted to optimize polygonValues much and 'raster' does
not do multi-processor computations. I hope to have that implemented,
at least for some slower functions like this one, by the end of this
year.

Robert

On Wed, Jun 30, 2010 at 7:12 AM, Agustin Lobo <alobolistas at gmail.com> wrote:
> Hi!
> I'm trying:
>
>> eugrd025EFDC <- readOGR(dsn="eugrd025EFDC",layer="eugrd025EFDC")
> v <- polygonValues(p=eugrd025EFDC, Br, weights=TRUE)
>
> where
>
>> str(eugrd025EFDC,max.level=2)
> Formal class 'SpatialPolygonsDataFrame' [package "sp"] with 5 slots
>  ..@ data       :'data.frame': 18000 obs. of  5 variables:
>  ..@ polygons   :List of 18000
>  .. .. [list output truncated]
>  ..@ plotOrder  : int [1:18000] 17901 17900 17902 17903 17899 17898
> 17904 17897 17905 17906 ...
>  ..@ bbox       : num [1:2, 1:2] 2484331 1314148 6575852 4328780
>  .. ..- attr(*, "dimnames")=List of 2
>  ..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slots
>
>> summary(Br)
> Cells:  13967442
> NAs  :  0
>
>
> Min.       0.00
> 1st Qu.    0.00
> Median     0.00
> Mean      48.82
> 3rd Qu.    0.00
> Max.    4999.00
>
> so quite large objects.
>
> The problem is that  polygonValues() has been running (and not
> completed the task) for
> more than 2 h on a intel core i7 machine with 16 Gb RAM (Dell
> Precision M6500), so a pretty powerful machine.
> Is there any way I could speed up this process?
> Also, is there anything I could do in order to take better advantage
> of the 8 processing threads?
> Currently, I see only 1 cpu working for R processes and the rest
> remain pretty inactive
>
> Thanks
>
> Agus
>
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