[R-sig-Geo] (no subject)

[Rainer M Krug]

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On 01/10/2011 06:48 PM, Giuseppe Amatulli wrote:
> Hi,
> first of all  happy new year!
> 
> I'm trying to do forest species distribution at European level (1 km
> resolution) by means of  randomForest running it in a cluster
> computer. I'm using several predictors of different data sources. All
> of them are rasters in grass format.  Therefore i was using spgrass6
> to import the data in to R and apply randomForest prediction to the
> layers.
> 
> In the same time, reading carefully the help page of the raster
> package seems to me that his "row by row" feature allows a better
> performance of the memory limitation, compare to spgrass6. It is this
> the case?
> If raster package is more efficient, how i can use it to import grass
> data?  I suppose by reading the raster under the cellhd folder
>>  maps  <-  stack ( c ( 'LOCATION/PERMANENT/cellhd/grid1','LOCATION/PERMANENT/cellhd/grid2'))

Another option would be to copy the data into a database, and then use
sql queries to select locations to analyse. In this way, you could have
more control over the number of cells to analyse. This obviously only
works, if you don't need neighbourhood information.

Cheers,

Rainer


> 
> One more question.
> The data for training randomforest are stored in R table. Each
> observation represent the  presence/absence ( 0 or 1 ) of a plant
> specie. I also have an item of presence/absence reliability which give
> to me information concerning the quality of the data. Whit this item i
> would like to give a "weight" in randForest in order to give more
> importance to the "good" data. Any idea?
> As rough  idea i was thinking to replicate the data in accordance to
> the quality but it this will increment to much the amount of data. On
> the opposite a stratified bootstrapping will result in a data
> squeezing and long computation.
> In other words i'm searching a weight options as present in lm model. Any idea?
> 
> Thank in advance
> Regards
> Giuseppe Amatulli
> 
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- -- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Natural Sciences Building
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Stellenbosch University
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email:      Rainer at krugs.de

Skype:      RMkrug
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