[R-sig-Geo] Performance SpatialGridDataFrame to rasterStack

[Johannes Signer]

Hello,

not sure if it works for you, but why not directly build a raster
stack (example below).

Hope this helps,
Johannes

# ---------------------------------------------------------------------------- #
library(raster)

# Create dummy data
r1 <- raster(nrows=1000, ncols=800, xmn=0, xmx=100)
r1 <- setValues(r1, rnorm(800000))

# write dummy rasters
sapply(1:60, function(x) writeRaster(r1, paste("r", x, ".tif",
sep=""), overwrite=T))

# Read read raster into a stack
system.time(r <- stack <- do.call("stack",
lapply(list.files(pattern="*.tif"), raster)))

# on a 3 GB netbook this took just a bit more than 11 seconds

On Fri, Mar 2, 2012 at 12:28 PM, Johannes Radinger <JRadinger at gmx.at> wrote:
> Hi,
>
> I want to use raster maps for Species Distribution Modelling (SDM) with
> the package 'dismo'. Therefore I load several rastermaps (around 60) with the readRAST6 command. For further processing I want to transform them into a raster stack. Each of the raster has the same spatial extent and the same resolution (per rastermap: around 765000 cells, thereof 760000 NA's, 5000 non null cells).
>
> The readRAST6 command to load all rasters in one step into a SpatialGridDataFrame works really good (1-2 min). The problem now is the tranformation into a stack. This takes very long time (I waited for 45 min), the CPU is mostly 100%, the pyhsical memory usage 3 GB (only a few MB left) and the virtual memory usage for R 3 GB, the HDD activity 20-30 MB/Sec data written. So my Computer seem to be at its maximum, and I don't have access to a faster/better one. I am doint all my R processes within an Eclipse workspace.
>
> What I do:
> rast <- readRAST6(rast.list, cat=(FALSE,length(rast.list)), ignore.stderr=TRUE, plugin=NULL)
>
> rast.stack <- stack(rast)
>
>
> Is there any way how I can improve the performance? As most of the raster cells are NULL cells maybe there is a special way consider that? Or splitting the SpatialGridDataFrame up and recombining the stacks in the end?
> Or saving substeps to the harddisk?
> Any help/suggestion is mostly welcome!
>
> Best regards,
> Johannes
>
> --
>
> Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a
>
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