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

[Roger Bivand]

On Thu, 26 Aug 2010, Michał Kwieciński wrote:

> 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.

Wrong. Display in edit.nb() was broken when the input nb included 
no-neighbour observations. I a separate reply I'll explain that you need 
to fix your broken shapefile.

Roger

>
> Thank you again,
> Michal
>
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-- 
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