[R-sig-Geo] raster::clump not working?

[Michael Treglia]

Check out SDMTools::ConnCompLabel
I think that will get you what you're after.

Hope that helps!
Mike


Please pardon any typos, this message was sent from a mobile device.

On Fri, May 25, 2018, 7:15 AM João Carreiras <jmbcarreiras using gmail.com> wrote:

> Dear Ben,
>
> Thank you for your prompt reply.
>
> Now I see what clump does. I just thought clump would give the same
> result as ArcGIS "Region Group". I need some command to assign a
> different value to each patch. And by patch I mean contiguous pixels
> having the same value, so that in this (absurd) example I would get
> 648 patches.
>
> Take care
> Joao
>
> On 25 May 2018 at 11:35, Ben Tupper <btupper using bigelow.org> wrote:
> > Hi,
> >
> > I think it is actually correct - there is only one 'clump' of connected
> > cells.  In raster clumps are separated from other clumps by backgound (0
> or
> > NA).  In your example there is no background anywhere so there is just
> one
> > clump.
> >
> > You can see the difference if you divide x in to halves with a row of
> NAs.
> > Note that limited spatial extent so the clumping doesn't wrap around the
> > globe which it will for [-180, 180].
> >
> > r <- raster(ncols=36, nrows=18, xmn = 0, xmx = 36, ymn = 0, ymx = 18)
> > x <- init(r, fun='cell')
> >
> > x[9,1:36] <- NA
> > y <- clump(x)
> > y
> > # class       : RasterLayer
> > # dimensions  : 18, 36, 648  (nrow, ncol, ncell)
> > # resolution  : 1, 1  (x, y)
> > # extent      : 0, 36, 0, 18  (xmin, xmax, ymin, ymax)
> > # coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
> > # data source : in memory
> > # names       : clumps
> > # values      : 1, 2  (min, max)
> >
> > x[1:18, 18] <- NA
> > y
> > # class       : RasterLayer
> > # dimensions  : 18, 36, 648  (nrow, ncol, ncell)
> > # resolution  : 1, 1  (x, y)
> > # extent      : 0, 36, 0, 18  (xmin, xmax, ymin, ymax)
> > # coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
> > # data source : in memory
> > # names       : clumps
> > # values      : 1, 4  (min, max)
> >
> >
> > Cheers,
> > Ben
> >
> >
> > On May 25, 2018, at 6:00 AM, João Carreiras <jmbcarreiras using gmail.com>
> wrote:
> >
> > Hi!
> >
> > I've been trying to run the clump command but the output is consistently
> a
> > raster with values == 1. Please find below an example.
> >
> > I'm sure I'm doing something stupid. However, the command is really
> > straightforward and I can't seem to identify what the problem might be.
> >
> > Any help really appreciated.
> > Thanks
> > Joao
> >
> > r <- raster(ncols=36, nrows=18)
> > x <- init(r, fun='cell')
> > x
> > class       : RasterLayer
> > dimensions  : 18, 36, 648  (nrow, ncol, ncell)
> > resolution  : 10, 10  (x, y)
> > extent      : -180, 180, -90, 90  (xmin, xmax, ymin, ymax)
> > coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
> > data source : in memory
> > names       : layer
> > values      : 1, 648  (min, max)
> > a <- clump(x)
> > a
> > class       : RasterLayer
> > dimensions  : 18, 36, 648  (nrow, ncol, ncell)
> > resolution  : 10, 10  (x, y)
> > extent      : -180, 180, -90, 90  (xmin, xmax, ymin, ymax)
> > coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
> > data source : in memory
> > names       : clumps
> > values      : 1, 1  (min, max)
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > R-sig-Geo using r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >
> >
> > Ben Tupper
> > Bigelow Laboratory for Ocean Sciences
> > 60 Bigelow Drive, P.O. Box 380
> > East Boothbay, Maine 04544
> > http://www.bigelow.org
> >
> > Ecological Forecasting: https://eco.bigelow.org/
> >
> >
> >
> >
> >
>
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