[R-sig-Geo] problem with edit.nb

Michał Kwieciński jamesbond6 at gmail.com
Thu Aug 26 20:54:17 CEST 2010

2010/8/26 Michał Kwieciński <jamesbond6 at gmail.com>:
> 2010/8/26 Roger Bivand <Roger.Bivand at nhh.no>:
>> On Thu, 26 Aug 2010, Michał Kwieciński wrote:
>>> 2010/8/26 Roger Bivand <Roger.Bivand at nhh.no>:
>>>> On Thu, 26 Aug 2010, Michał Kwieciński wrote:
>>>>> Hi all,
>>>>> I am just about to finish my thesis. The spatial model I want to use
>>>>> there is an extension of some work I did back in April. I used R 2.9.2
>>>>> then and in order to include 3 additional administrative areas for
>>>>> Poland, I edited the shp files (the borders aren't perfectly aligned).
>>>>> Then in R I created the nb class object and edited it with edit.nb
>>>>> adding three new connections. Everything worked perfect, I had no
>>>>> regions with no links and I generated weight matrices with no
>>>>> problems.
>>>>> However, I'd been doing exactly the same thing entire night in R 2.11
>>>>> and it did not work (I use the same code I did 4 months ago) and I
>>>>> have no idea what is the reason for it. I've been looking for some
>>>>> other way to do it, I tried nb2mat and editing the matrix, but I
>>>>> surrendered having no idea where and what values I should use.
>>>>> Before editing nb object R claims that regions 377 and 378 have no
>>>>> links. However in edit.nb the 378 and 379 are visible as having no
>>>>> links (378 and 379 are cities added on top of bigger shapes, whereas
>>>>> 377 was just split from a bigger shape into two smaller ones and only
>>>>> the link between these two parts is missing). I connect the circles,
>>>>> quit and in the new object there are some new links - the overall
>>>>> number has increased - but 377 and 378 are still listed as having no
>>>>> links. Editing nb again shows the links, so they have been saved for
>>>>> sure.
>>>>> I am not an advanced R user and most of my code was based on my
>>>>> professor's book. However, I think I have spent enough time with
>>>>> spatial models and those matrices in order to call this problem really
>>>>> weird. Especially since it worked perfectly last time...
>>>>> I can attach shp files and my code if it will be of any help in order
>>>>> to properly investigate this problem. I would really appreciate some
>>>>> help, I need to finish the project over the weekend.
>>>> Maybe you are using the wrong indices, as FIDs are 0-base but nb objects
>>>> are
>>>> 1-base. So you may be editing the wrong ones. If this doesn't resolve the
>>>> problem, zip the shapefile and post a link to it, don't attach the
>>>> shapefile, as it would be sent to 1700 people.
>>> I must admit I did not understand your hint (I do not know what "base"
>>> is, assuming FID is Field ID - header in shp file). How is it possible
>>> I edited some other layer of information by function edit.nb? Could
>>> you please clarify what should I do to check it?
>> Google "0-based" gets you to Wikipedia:
>> "0 (zero-based indexing)
>>    The first element of the array is indexed by subscript of 0.
>> 1 (one-based indexing)
>>    The first element of the array is indexed by subscript of 1."
>> So the FIDs in the shapefile are 0, ..., (n-1), and identify the
>> observations, so are set in the region.id attribute of the nb object. Then
>> if print(nb) says that "377" and "378" have no neighbours, and the region.id
>> values are from the shapefile:
>> which(card(nb) == 0)
>> will likely say 378 379, and
>> attr(nb, "region.id")[which(card(nb) == 0)]
>> will say "377" "378".
>> The indices used internally in edit.nb are the 1-based indices. They
>> probably should be the ones stored in the region.id attribute, but this
>> would involve an extra level of indexing. If you don't understand, put the
>> shapefile on a website and post the link.
> Ok, now I understand. This is true in my case - it explains why I see
> different numbers in listing of "no-links regions" and on the map in
> edit.nb. That brings me only to the main question: why, even after
> connecting the nodes (and verifying they are connected with plot.nb),
> the print(nb) still says that those two regions remain unconnected?
> http://home.elka.pw.edu.pl/~mkwiecin/edit.nb-problem.rar
> I uploaded here the code I use, maps and two screens explaining where
> to look for the missing links in question.

Ok, I did what I should have done at the very beginning (I even gave
myself a hint to do that on the beginning of my first message...).
Anyway, installed R 2.9.2 again and it appears to be working correctly
- no missing links after edit.nb().

I do not know what author of this (
https://stat.ethz.ch/pipermail/r-sig-geo/2010-July/008908.html )
message meant, but I suppose he had the same problem.

I will continue working on 2.9.2 version, so by now I am grateful for
your help Roger, but I don't think it is necessary to investigate in
hurry why edit.nb does not work in 2.11.

Thank you again,

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