[R-sig-Geo] sp::disaggregate() does not seem to add the necessary "comment" attribute to identify holes if Polygons does not contain exactly 1 polygon with 0 or 1 holes

[Roger Bivand]

On Sat, 29 Apr 2017, Anne C. Hanna wrote:

> Roger,
>
> This looks great, and I will try it out ASAP.  I do have one reservation 
> though --- it seems you are using createSPComment() to reconstruct the 
> comments, and I have seen some discussion that that may not be reliable 
> in all cases (e.g. if the initial polygons are wonky in some way).  I 
> don't know a lot about this, but is it possible that it would be 
> preferable to parse and appropriately disaggregate the original comments 
> strings (if they exist), so as to deal slightly more smoothly with such 
> cases (i.e., the polygons would still be wonky, but at least the 
> hole/polygon matching would track with whatever was in the original 
> data)?

Contributions very welcome - this was code moved from the raster package, 
so I really have little feeling for why it is necessary.

Please provide references and use cases. GEOS is strict in its treatments 
of geometries, but does work in most cases. People just expressing 
opinions doesn't help, and may well be misleading. It is possible to clean 
geometries too, see the cleangeo package. createPolygonsComment probably 
isn't foolproof, but specific reports help, because then it is possible to 
do something about it. sp classes didn't use simple features when written 
because sf was not widely used then - introduced in 2004, when sp was 
being developed. Using sf helps, and rgeos::createPolygonsComment was a 
work-around from 2010 when rgeos was written.

Even when you use sf in the sf package, you will still run into invalid 
geometries because the geometries are in fact invalid, the sf package 
also uses GEOS.

Roger

>
> I also had no success using createSPComment to fix disaggregate()'s 
> output previously, even though my polygons are perfectly non-wonky, so I 
> am perhaps a little more untrusting of it than I should be.  But I'll 
> let you know how this version works with my data.  Thanks for addressing 
> this so quickly!
>
> - Anne
>
>
> On 04/28/2017 12:11 PM, Roger Bivand wrote:
>> I've pushed the fix to my fork:
>>
>> https://github.com/rsbivand/sp
>>
>> and created a pull request:
>>
>> https://github.com/edzer/sp/pull/28
>>
>> Only one part of a complicated set if nested if() in disaggregate() was adding
>> comments, but in some settings the existing comments survived the
>> disaggregation. Now the Polygons object comment attribute is re-created for
>> all Polygons objects. This is version 1.2-6, also including code changes that
>> internally affect rgdal and rgeos - you may like to re-install them from
>> source after installing this sp version (shouldn't matter).
>>
>> Roger
>>
>> On Fri, 28 Apr 2017, Anne C. Hanna wrote:
>>
>>> Hello.  I first posted this issue report on the sp GitHub repo
>>> (https://github.com/edzer/sp/issues/27) and it was suggested that I redirect
>>> it to here.
>>>
>>> I am working with a geographic dataset with complex borders. The data is
>>> stored as a SpatialPolygonsDataFrame.  Each Polygons object in the data frame
>>> may be composed of multiple disjoint polygons, and each polygon may have
>>> multiple holes.  I want to disaggregate each of the Polygons objects into its
>>> individual disjoint polygons and construct an adjacency matrix for all the
>>> disjoint components, and I was using disaggregate() to do this.  However, when
>>> I run gTouches() on the disaggregated data, in order to compute the
>>> adjacencies, I get a number of warnings like this:
>>>
>>> Error in RGEOSBinPredFunc(spgeom1, spgeom2, byid, "rgeos_touches") : Polygons
>>> object missing comment attribute ignoring hole(s).  See function
>>> createSPComment.
>>>
>>> Looking at the Polygons "comment" attributes in the SpatialPolygonsDataFrame
>>> output by disaggregate(), I see that the only comment values are "0"
>>> (indicating a single polygon with no holes), "0 1" (indicating a single
>>> polygon with a single hole), and NULL (apparently no comment was written).
>>> Since I know my dataset contains several Polygons objects which are composed
>>> of multiple disjoint regions, and also several Polygons which contain more
>>> than one hole, this is not the expected result.  In reading the disaggregate()
>>> code in the sp GitHub repository (specifically, explodePolygons()), I also
>>> can't see anywhere the comment is being added for the cases where a Polygons
>>> object has more than two parts or more than two holes.  It actually seems like
>>> it's getting carried along almost accidentally in the few cases that do get
>>> comments, and neglected otherwise.
>>>
>>> Assuming I'm not failing to understand the code and the desired behavior
>>> (entirely possible, as I am new at working with this software!), this seems
>>> suboptimal to me.  My dataset is pretty well-behaved (despite its complexity),
>>> so I should be able to fix my issues with judicious application of
>>> createPolygonsComment.  But I had a heck of a time figuring out what was going
>>> wrong with gTouches, since Polygons comment management appears to be a pretty
>>> obscure field (and createSPComment wasn't working for me, for whatever
>>> reason).  So it seems like it might be better if disaggregate() just parses
>>> and passes along the comments from its input correctly, or, if it's absolutely
>>> necessary to not create comments, passes nothing and warns clearly in the
>>> manual that comments and associated hole information are being lost.  Passing
>>> along comments in some cases while silently dropping them in others seems like
>>> kind of the worst of both worlds.
>>>
>>> I've attached a set of tests I wrote to demonstrate desired/undesired
>>> behavior: disaggregate_comment_tests.R.  My R version is 3.4.0, my sp version
>>> is 1.2-4, my rgeos version is 0.3-23 (SVN revision 546), and my GEOS runtime
>>> version is 3.5.1-CAPI-1.9.1 r4246.  I am using Debian Release 9.0 with kernel
>>> version 4.9.0-2-amd64.  I hope this is useful; please let me know if you need
>>> more info or if there is a better place to post this issue.
>>>
>>> - Anne
>>>
>>
>
>

-- 
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger.Bivand at nhh.no
Editor-in-Chief of The R Journal, https://journal.r-project.org/index.html
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