[R-sig-Geo] problem with rasterToPolygons x worldclim

[Michael Sumner]

On Thu, 7 Apr 2016 at 00:33 Michael Sumner <mdsumner at gmail.com> wrote:

> On Thu, 7 Apr 2016 at 00:22 Michael Sumner <mdsumner at gmail.com> wrote:
>
>> On Wed, 6 Apr 2016 at 23:45 Karla Shikev <karlashikev at gmail.com> wrote:
>>
>>>
>>> Hi Michael,
>>>
>>> Thanks for the tips. I tried the help for rasterToPolygons, but none of
>>> the options (e.g. dissolve=TRUE) made any difference. I tried gPolygonize
>>> and it worked, except for (as you predicted), if the edges meet the raster
>>> extents - but that definitely was an advance!
>>>
>>>
>> I see the issue, the fun argument to rasterToPolygons is masking out
>> values from that interval, but it's not setting them all to the same value
>> - so you still get individual pixel polygons unless you mask on presence in
>> the interval or not (as a binary):
>>
>> library(raster)
>>
>> r<-getData('worldclim', var='bio', res=10)$bio1
>>
>> e <- extent(-140,-100, 50, 60)
>>
>> xx <- crop(r,e)
>> ## mask out pixel values first
>> xx <- xx > 40 & xx < 60
>>
>> ## 576 polygons
>> slice1<- rasterToPolygons(xx, fun = function(x) {x == 1})
>> ## 1 polygon
>> slice2 <- rasterToPolygons(xx,  fun = function(x) {x == 1}, dissolve =
>> TRUE)
>>
>>
>> Still it's not a very nice polygon, if I can I'll try a different way.
>>
>> Cheers, Mike.
>>
>>
>>
>>
>
> You can use tricks to fill the outer edge so you get a valid contour line
> all the way around (it's not always going to work - see here for the
> explanation by whuber:
> http://gis.stackexchange.com/questions/61550/colouring-areas-between-vector-contours
> )
>
>

Sorry, forgot the code!

library(raster)

r<-getData('worldclim', var='bio', res=10)$bio1

e <- extent(-140,-100, 50, 60)

xx <- crop(r,e)

## buffer out a little
xx2 <- extend(xx, extent(xx) + res(xx) * 4, value = NA_real_)

## set missing to less than interval
xx2[is.na(xx2)] <- cellStats(xx2, min)
## now contour
cl <- rasterToContour(xx2 > 40 & xx2 < 60, level = 1)

pp <- rgeos::gUnionCascaded(rgeos::gPolygonize(cl))
pp
plot(pp, col = "grey")




> Is this better? Maybe - there are lots of other ways - maybe a buffer on
> this gives roughly what you need. Maybe you only need a total area so
> summing pixels after filtering is better?
>
> Would be nice to have contouring that reliably produced polygons, but it's
> a tricky problem. Other kinds of shape-finding might be better, with
> alphahull on the pixel points perhaps, but you quickly get into "geometry
> fudger" territory here rather than objective measures.
>
> HTH
>
>
>
>
>>
>>>
>>> I really appreciate your help and if you just point the way I can try to
>>> go after what needs to be done, but right now I´m stumped.
>>>
>>> best, Karla.
>>>
>>> On Mon, Apr 4, 2016 at 5:38 PM, Michael Sumner <mdsumner at gmail.com>
>>> wrote:
>>>
>>>> Read the help for rasterToPolygons, alternatively try chaining
>>>> rasterToContour and rgeos::gPolygonize.
>>>>
>>>> The latter may need coaxing if your edges meet the raster extents.
>>>>
>>>> Cheers, Mike
>>>>
>>>> On Tue, 5 Apr 2016, 05:32 Karla Shikev <karlashikev at gmail.com> wrote:
>>>>
>>>>> Dear all,
>>>>>
>>>>> Here's an issue that is related to the previous one. In the commands
>>>>> below
>>>>> I'm trying to make a polygon for all the regions within a range of mean
>>>>> annual temps. However, rasterToPolygons will draw a square around each
>>>>> value in the original raster, rather than providing me the actual
>>>>> polygon,
>>>>> given that resolution. Any hints? Again, any help will be greatly
>>>>> appreciated.
>>>>>
>>>>> Karla
>>>>>
>>>>> _____
>>>>>
>>>>> library(raster)
>>>>>
>>>>> r<-getData('worldclim', var='bio', res=10)$bio1
>>>>>
>>>>> e <- extent(-140,-100, 50, 60)
>>>>>
>>>>> xx<-crop(r,e)
>>>>>
>>>>> slice1<-rasterToPolygons(xx, fun = function(x) {x > 40 & x < 60})
>>>>>
>>>>> plot(slice1)
>>>>>
>>>>>         [[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
>>>>>
>>>> --
>>>> Dr. Michael Sumner
>>>> Software and Database Engineer
>>>> Australian Antarctic Division
>>>> 203 Channel Highway
>>>> Kingston Tasmania 7050 Australia
>>>>
>>>>
>>> --
>> Dr. Michael Sumner
>> Software and Database Engineer
>> Australian Antarctic Division
>> 203 Channel Highway
>> Kingston Tasmania 7050 Australia
>>
>> --
> Dr. Michael Sumner
> Software and Database Engineer
> Australian Antarctic Division
> 203 Channel Highway
> Kingston Tasmania 7050 Australia
>
> --
Dr. Michael Sumner
Software and Database Engineer
Australian Antarctic Division
203 Channel Highway
Kingston Tasmania 7050 Australia

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