[R-sig-Geo] readRAST6() in {spgrass6}

[Sam Prentice]

Thanks for the help. I understand there are more elegant and efficient
approaches to classification, and they are becoming more clear in time, out
of experience and necessity of my research. Such is learning. Nonetheless,
I'm also fairly confident about what I'm trying to achieve in the moment (a
classified landform element map), why (to guide representative soil sampling
of said landform elements), and what my constraints are (impending soil dry
down). I assumed incorrectly that a published approach could be emulated not
with ease, but without a several month time commitment. Please excuse my
naiveté in regards to the tools, and thanks again for your feedback.

Sam 

|-----Original Message-----
|From: Roger Bivand [mailto:Roger.Bivand at nhh.no]
|Sent: Monday, May 16, 2011 9:28 PM
|To: Sam Prentice
|Cc: Dylan Beaudette; r-sig-geo at r-project.org
|Subject: Re: [R-sig-Geo] readRAST6() in {spgrass6}
|
|On Mon, 16 May 2011, Dylan Beaudette wrote:
|
|> It is hard to know what the upper-limit is on Windows-- as the memory
|> is usually fragmented by the operating system.
|
|Correct, the upper limit on other OS is higher in practice.
|
|>
|> Since you are using GRASS, I would first try a coarsened version of
|> your terrain-shape rasters via the built-in re-sampling functionality.
|> While this is not ideal, as it is NN-based, it will give a quick way
|> to try out methods.
|>
|> After you have initialized your GRASS connection in R, execute something
|like:
|>
|> system('g.region res=10 -ap')
|>
|> This will align the region along a 10x10 map unit grid. All further
|> interaction with raster data will be automatically re-sampled to this
|> grid system.
|
|Right, for some res=, you will get a systematic sample that will let you
|decimate your data. Randomly shifting the window while resampling will help
|you see whether your classification model boundaries change.
|
|As both Dylan and I have said, there is no good reason for calibrating the
|classification model with more data than necessary, even if it were
possible.
|The only reason to use very much data would be if discrimination between
|very rare classes is your target, but even then you could stratify your
sample
|to get better representation of critical areas.
|
|You seem to be looking for classification signatures, from which you are
going
|to predict. Sampling will give you distributions of these signatures, which
could
|be used for similation by tile. If you are very concerned about the
statistical
|quality of your classification signatures, you could go fuzzy, but your
main goal
|is to get to the distributions of these signatures, IMO. Once you have
them,
|you can predict. You do not need to have GBs of dat in memory to do this
|adequately.
|
|So one could agree that software (OS, R, whatever) is your limitation, but
it is
|only a limitation if you are not able to consider more statistical
approaches to
|your apparent problem, which is finding out how to classify your input, and
|then to predict to output.
|
|Roger
|
|>
|> Dylan
|>
|> On Mon, May 16, 2011 at 2:25 PM, Sam Prentice <sep at umail.ucsb.edu>
|wrote:
|>> Thanks you for your suggestions. This error is not affected by choice
|>> of mapset, and is not limited by my hardware.
|>>
|>> Further info: I'm running 64-bit windows, 16MB memory, w/multiple cores.
|>> GRASS 6.4.1, R 2.12.2. I'm running standalone R using initGRASS() to
|>> set GRASS env parameters. The GRASS files I'm trying to read-in are
|>> DEM derivatives, each ~170MB. The intermediate .tmp file in the error
|>> message is 300MB.
|>>
|>> It's been suggested that I am "likely trying to import too much data
|>> into R". Assuming non-limiting computer power, what is the upper
|>> bound on amount of data that can be read into R from GRASS? If not a
|>> fixed amount, what are the main conditions that cause it to vary? I
|>> did not see this addressed in the {spgrass6} documentation, so I'm
|>> assuming it's a base R limitation, but maybe not? Quantifying this
|>> limitation will help determined how to move forward (e.g, resampling
|>> at smaller scale versus subsetting my DEM derivatives).
|>>
|>> Thanks,
|>> Sam
|>>
|>> |-----Original Message-----
|>> |From: Pierre Roudier [mailto:pierre.roudier at gmail.com]
|>> |Sent: Tuesday, May 10, 2011 3:40 PM
|>> |To: Sam Prentice
|>> |Cc: r-sig-geo at r-project.org
|>> |Subject: Re: [R-sig-Geo] readRAST6() in {spgrass6}
|>> |
|>> |Could that message have anything to do with the fact that this is a
|>> |layer
|>> from
|>> |the PERMANENT mapset?
|>> |
|>> |My two cents,
|>> |
|>> |Pierre
|>> |
|>> |2011/5/11 Sam Prentice <sep at umail.ucsb.edu>:
|>> |> Hi,
|>> |>
|>> |>
|>> |>
|>> |> I'm running R 2.12.2 via Tinn-R on Windows Server 2008. I'm using
|>> |> R for cluster analysis for terrain classification and I'm getting
|>> |> the following error when parsing GRASS data into R:
|>> |>
|>> |>
|>> |>
|>> |>> x =
|>> |>
|>>
||readRAST6(c("param_elev3","param_crosC_1m","param_longC_1m","para
|m
|>> |_slope5","
|>> |> param_profC","param_miniC_1m","param_maxiC_1m"))
|>> |>
|>> |> D:/GRASSdata/Sedgwick2/PERMANENT/.tmp/param_elev3 has GDAL
|driver
|>> |> GTiff
|>> |>
|>> |> and has 6224 rows and 6242 columns
|>> |>
|>> |>
|>> |>
|>> |> Error in deleteDataset(DS) :
|>> |>
|>> |>                GDAL Error 1: Deleting
|>> |> D:/GRASSdata/Sedgwick2/PERMANENT/.tmp/param_elev3 failed:
|>> |>
|>> |> Permission denied
|>> |>
|>> |>
|>> |>
|>> |> On the surface this looked like an issue with user privileges,
|>> |> since I do not have admin-level user privileges on this machine.
|>> |> However, this has been corrected - I now have permissions on the
|>> |> .tmp directory listed in the error, and I can create, append, and
|>> |> delete any file in that location, but the error is still occurring.
|>> |>
|>> |>
|>> |>
|>> |> Thoughts?
|>> |>
|>> |>
|>> |>
|>> |> Thanks,
|>> |>
|>> |> Sam
|>> |>
|>> |>
|>> |>        [[alternative HTML version deleted]]
|>> |>
|>> |> _______________________________________________
|>> |> R-sig-Geo mailing list
|>> |> R-sig-Geo at r-project.org
|>> |> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
|>> |>
|>> |
|>> |
|>> |
|>> |--
|>> |Scientist
|>> |Landcare Research, New Zealand
|>>
|>> _______________________________________________
|>> R-sig-Geo mailing list
|>> R-sig-Geo at r-project.org
|>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
|>>
|>
|> _______________________________________________
|> R-sig-Geo mailing list
|> R-sig-Geo at r-project.org
|> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
|>
|
|--
|Roger Bivand
|Economic Geography Section, Department of Economics, Norwegian School of
|Economics and Business Administration, Helleveien 30, N-5045 Bergen,
|Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
|e-mail: Roger.Bivand at nhh.no