I couldn't get either script to run on my home computer this morning.  My
version of raster was even older on this computer.

I updated the package and now both scripts are running like a charm.  My
home PC has 8 GB of RAM compared to my work PC's 16 GB.  If I don't post
again, and update at work got it to run.

Does the benefit of init() lie in this line from the help article? "cell
values are initialized without reference to pre-existing values"making it
faster?

Thanks for your help,
Andrew


On Tue, Jul 16, 2013 at 3:37 PM, Robert J. Hijmans <r.hijmans@gmail.com>wrote:

> Andrew,
>
>
> A simpler script that works for me (indeed with the version of raster)
>
> library(raster)
> r <- raster(xmn =  688256.5, xmx = 779259.5, ymn = 4276005, ymx =
> 4396000, nrows = 11650, ncols = 11347, crs = "+proj=utm +zone=11
> +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0")
> set.seed(232)
> r <- init(r, function(x) runif(x, min = 1352, max = 3981),
> filename='r_from_File.grd', overwrite = TRUE)
> rough <- terrain(r, opt = 'roughness', filename =
> 'roughness_test.grd', overwrite = TRUE)
>
>
> If this uses too much RAM for your computer, then use a more
> conservative chunksize. Set it to e.g.
>
> rasterOptions(chunksize=1e+06)
> # and do
> r <- raster('r_from_File.grd')
> rough <- terrain(r, opt = 'roughness', filename =
> 'roughness_test.grd', overwrite = TRUE)
>
> Robert
>
> On Tue, Jul 16, 2013 at 2:31 PM, Michael Sumner <mdsumner@gmail.com>
> wrote:
> > That's a pretty old version of raster (released over a month ago :).
> >
> > FWIW, I can run your code successfully with the latest CRAN version so
> > perhaps see if that fixes the issue first.
> >
> > (sessionInfo below)
> >
> > Cheers, Mike.
> >
> > R version 3.0.1 Patched (2013-07-07 r63210)
> > Platform: x86_64-w64-mingw32/x64 (64-bit)
> >
> > locale:
> > [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
> > [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
> > [5] LC_TIME=English_Australia.1252
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  compiler  methods
> > [8] base
> >
> > other attached packages:
> > [1] raster_2.1-49 sp_1.0-11
> >
> > loaded via a namespace (and not attached):
> > [1] grid_3.0.1      lattice_0.20-15
> >
> >
> >
> > On Wed, Jul 17, 2013 at 6:22 AM, Andrew Vitale <vitale232@gmail.com>
> wrote:
> >> Hello,
> >>
> >> I'm getting some strange behavior from the raster package terrain(opt =
> >> 'roughness') function.
> >>
> >> I have a large (~1GB) digital elevation model in .grd format that was
> >> created from a past R session.  When I load the file in and attempt to
> >> calculate the roughness index, I consistently crash R.
> >>
> >> In an attempt to debug, I created a raster file with the same extent,
> >> nrows, ncols, and crs as my actual data, and set random values with the
> >> same min and max.  My system is storing the file in memory rather than
> >> writing to the temporary library.  The terrain(opt = 'roughness')
> function
> >> sometimes runs with the raster in RAM, but usually doesn't.
> >>
> >> Since running from memory doesn't help me with my problem, I've created
> the
> >> sample script to save the simulated DEM to disk then exit R without
> saving
> >> the session.  You'll then have to restart R.  The second part of the
> code
> >> attempts to reload the simulated DEM and calculate roughness, and this
> >> piece of code crashes every time I run it (as it does with my actual
> data).
> >>
> >> Here is my sessionInfo(), and a sample code follows:
> >>
> >>
> >> R version 3.0.1 (2013-05-16)
> >> Platform: x86_64-w64-mingw32/x64 (64-bit)
> >>
> >> locale:
> >> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> >> States.1252
> >> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> >>
> >> [5] LC_TIME=English_United States.1252
> >>
> >> attached base packages:
> >> [1] stats     graphics  grDevices utils     datasets  methods   base
> >>
> >> other attached packages:
> >> [1] raster_2.1-37 sp_1.0-9
> >>
> >> loaded via a namespace (and not attached):
> >> [1] grid_3.0.1      lattice_0.20-15
> >>
> >>
> >>
> #===============================================================================
> >> #Example code
> >> #Set the working directory to your system
> >>
> #===============================================================================
> >> setwd('C:/Users/avitale/Documents')
> >> library(raster)
> >>
> >> #set the extent, resolution, and crs to match my data
> >> r <- raster(xmn =  688256.5, xmx = 779259.5, ymn = 4276005, ymx =
> 4396000,
> >> nrows = 11650, ncols = 11347,
> >> crs = "+proj=utm +zone=11 +datum=WGS84 +units=m +no_defs +ellps=WGS84
> >> +towgs84=0,0,0")
> >>
> >> set.seed(232)
> >> r[] <- runif(ncell(r), min = 1352, max = 3981)
> >>
> >> #Write r to disk and exit the r session without saving
> >> r <- writeRaster(r, 'r_from_File.grd', overwrite = TRUE)
> >> q(save = 'no')
> >>
> >>
> #===============================================================================
> >> #Restart R!!!
> >> #Set the working directory to your system
> >>
> #===============================================================================
> >> setwd('C:/Users/avitale/Documents')
> >> library(raster)
> >>
> >> r <- raster(file.path(getwd(), 'r_from_File.grd'))
> >> rough <- terrain(r, opt = 'roughness', filename = 'roughness_test.grd',
> >> overwrite = TRUE)
> >>
> >>
> >>
> >> --
> >> *Andrew P. Vitale*
> >> Masters Student
> >> Department of Geography
> >> University of Nevada, Reno
> >> (412) 915-3632
> >> vitale232@gmail.com
> >>
> >>         [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> R-sig-Geo mailing list
> >> R-sig-Geo@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >
> >
> >
> > --
> > Michael Sumner
> > Hobart, Australia
> > e-mail: mdsumner@gmail.com
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > R-sig-Geo@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>



-- 
*Andrew P. Vitale*
Masters Student
Department of Geography
University of Nevada, Reno
(412) 915-3632
vitale232@gmail.com

	[[alternative HTML version deleted]]

