dnearneigh() from spdep: Points with the exact same location are not considered neighbours.

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dnearneigh() from spdep: Points with the exact same location are not considered neighbours.

R-sig-geo mailing list
Dear List

As I was working on a project, I realized that when I use dnearneigh
from spdep, two (or more) points that have the exact same coordinates
are not considered neighbours and thus are not linked (even when the
lower bound is put to 0 or even to -1). See below for an example.
(However this does not happen if the parameter longlat is set to false)

 Does the function behave the same way for you? Am I missing something?
Is this an expected behavior? And if so, if there a way to change that ?

In the example below, points 1 and 2 are not connected to each other/are
not neighbours (as you can see since the both have only one link, to 3),
even though they have the exact same coordinates (and are thus less than
25km apart), while point 3 is connected to both point 1 and 2.
If I want to assess autocorrelation using, for instance joincount.test,
this is then an issue...

>/library(data.table) />/library(spdep) />/pointstable <- data.table(XCoord=c(13.667029,13.667029,13.667028), /YCoord=c(42.772396,42.772396,42.772396))
>/print(pointstable) /     XCoord  YCoord
1: 13.667029 42.772396
2: 13.667029 42.772396
3: 13.667028 42.772396
>/coords <-cbind(pointstable$XCoord, pointstable$YCoord) />/nbLocal<- dnearneigh(coords, d1=0, d2=25, longlat = TRUE) />/nbLocal<- dnearneigh(coords, d1=-1, d2=25, longlat = TRUE) #both lines /produce the same output
>/summary(nbLocal) /Neighbour list object:
Number of regions: 3
Number of nonzero links: 4
Percentage nonzero weights: 44.44444
Average number of links: 1.333333
Link number distribution:

1 2
2 1
2 least connected regions:
1 2 with 1 link
1 most connected region:
3 with 2 links
>//
Thanks
Maël


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Re: dnearneigh() from spdep: Points with the exact same location are not considered neighbours.

Roger Bivand
Administrator
Do not post HTML-mail, only plain text. Your example is not reproducible
because you used HTML-mail.

Please read the help file, the bounds are described as being between lower
(greater than) and upper (less than or equal to) bounds. Since the
distance between identical points is strictly zero, they are not
neighbours because the distance must be > d1 and <= d2. If d1 is < 0, it
is reset to 0, as it is assumed that a negative lower bound is a user
error (and it would break the underlying compiled code).

In any case, no reasonable cross-sectional spatial process has duplicated
point (nugget) observations in situations in which spatial weights would
be used (spatio-temporal panels will have, but then time differs).

Hope this clarifies,

Roger

On Wed, 12 Apr 2017, Maël Le Noc via R-sig-Geo wrote:

> Dear List
>
> As I was working on a project, I realized that when I use dnearneigh
> from spdep, two (or more) points that have the exact same coordinates
> are not considered neighbours and thus are not linked (even when the
> lower bound is put to 0 or even to -1). See below for an example.
> (However this does not happen if the parameter longlat is set to false)
>
> Does the function behave the same way for you? Am I missing something?
> Is this an expected behavior? And if so, if there a way to change that ?
>
> In the example below, points 1 and 2 are not connected to each other/are
> not neighbours (as you can see since the both have only one link, to 3),
> even though they have the exact same coordinates (and are thus less than
> 25km apart), while point 3 is connected to both point 1 and 2.
> If I want to assess autocorrelation using, for instance joincount.test,
> this is then an issue...
>
>> /library(data.table) />/library(spdep) />/pointstable <- data.table(XCoord=c(13.667029,13.667029,13.667028), /YCoord=c(42.772396,42.772396,42.772396))
>> /print(pointstable) /     XCoord  YCoord
> 1: 13.667029 42.772396
> 2: 13.667029 42.772396
> 3: 13.667028 42.772396
>> /coords <-cbind(pointstable$XCoord, pointstable$YCoord) />/nbLocal<- dnearneigh(coords, d1=0, d2=25, longlat = TRUE) />/nbLocal<- dnearneigh(coords, d1=-1, d2=25, longlat = TRUE) #both lines /produce the same output
>> /summary(nbLocal) /Neighbour list object:
> Number of regions: 3
> Number of nonzero links: 4
> Percentage nonzero weights: 44.44444
> Average number of links: 1.333333
> Link number distribution:
>
> 1 2
> 2 1
> 2 least connected regions:
> 1 2 with 1 link
> 1 most connected region:
> 3 with 2 links
>> //
> Thanks
> Maël
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: [hidden email]
Editor-in-Chief of The R Journal, https://journal.r-project.org/index.html
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
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Re: dnearneigh() from spdep: Points with the exact same location are not considered neighbours.

R-sig-geo mailing list
Dear Roger,
Thank you for your answer, (And sorry for the HTML posting).

The issue persists if I specify "GE" for the lower bound, but only when
the parameter latlong is set to TRUE (see example below).


Regarding the nature of my data, it is a series of record of Jews
arrested during the Holocaust in Italy. Those are point data, and some
people have been arrested at the same place and at the same time (hence
my problem). I am trying to assess spatial autocorrelation for a binary
attribute (whether they survived the Holocaust or not), and I plan to
use a Join-count method, for which I need a spatial weight matrix. Is
using Join-count on such a dataset wrong ?

Best



Code:

library(data.table)
library(spdep)
pointstable <- data.table(XCoord=c(13.667029,13.667029,13.667028),
YCoord=c(42.772396,42.772396,42.772396))
print(pointstable)
coords <-cbind(pointstable$XCoord, pointstable$YCoord)
nbLocal<- dnearneigh(coords, d1=0, d2=25, longlat = TRUE, bound =
c("GE", "LE"))
summary(nbLocal)
nbLocal<- dnearneigh(coords, d1=0, d2=25, longlat = FALSE, bound =
c("GE", "LE"))
summary(nbLocal)


Output:
> print(pointstable)
     XCoord  YCoord
1: 13.66703 42.7724
2: 13.66703 42.7724
3: 13.66703 42.7724

> nbLocal<- dnearneigh(coords, d1=0, d2=25, longlat = TRUE, bound =
c("GE", "LE"))
> summary(nbLocal)
Neighbour list object:
Number of regions: 3
Number of nonzero links: 4
Percentage nonzero weights: 44.44444
Average number of links: 1.333333
Link number distribution:

1 2
2 1
2 least connected regions:
1 2 with 1 link
1 most connected region:
3 with 2 links

> nbLocal<- dnearneigh(coords, d1=0, d2=25, longlat = FALSE, bound =
c("GE", "LE"))
> summary(nbLocal)
Neighbour list object:
Number of regions: 3
Number of nonzero links: 6
Percentage nonzero weights: 66.66667
Average number of links: 2
Link number distribution:

2
3
3 least connected regions:
1 2 3 with 2 links
3 most connected regions:
1 2 3 with 2 links



On 12/04/2017 02:27, Roger Bivand wrote:

> Do not post HTML-mail, only plain text. Your example is not reproducible
> because you used HTML-mail.
>
> Please read the help file, the bounds are described as being between
> lower (greater than) and upper (less than or equal to) bounds. Since the
> distance between identical points is strictly zero, they are not
> neighbours because the distance must be > d1 and <= d2. If d1 is < 0, it
> is reset to 0, as it is assumed that a negative lower bound is a user
> error (and it would break the underlying compiled code).
>
> In any case, no reasonable cross-sectional spatial process has
> duplicated point (nugget) observations in situations in which spatial
> weights would be used (spatio-temporal panels will have, but then time
> differs).
>
> Hope this clarifies,
>
> Roger
>
> On Wed, 12 Apr 2017, Maël Le Noc via R-sig-Geo wrote:
>
>> Dear List
>>
>> As I was working on a project, I realized that when I use dnearneigh
>> from spdep, two (or more) points that have the exact same coordinates
>> are not considered neighbours and thus are not linked (even when the
>> lower bound is put to 0 or even to -1). See below for an example.
>> (However this does not happen if the parameter longlat is set to false)
>>
>> Does the function behave the same way for you? Am I missing something?
>> Is this an expected behavior? And if so, if there a way to change that ?
>>
>> In the example below, points 1 and 2 are not connected to each other/are
>> not neighbours (as you can see since the both have only one link, to 3),
>> even though they have the exact same coordinates (and are thus less than
>> 25km apart), while point 3 is connected to both point 1 and 2.
>> If I want to assess autocorrelation using, for instance joincount.test,
>> this is then an issue...
>>
>>> /library(data.table) />/library(spdep) />/pointstable <-
>>> data.table(XCoord=c(13.667029,13.667029,13.667028),
>>> /YCoord=c(42.772396,42.772396,42.772396))
>>> /print(pointstable) /     XCoord  YCoord
>> 1: 13.667029 42.772396
>> 2: 13.667029 42.772396
>> 3: 13.667028 42.772396
>>> /coords <-cbind(pointstable$XCoord, pointstable$YCoord) />/nbLocal<-
>>> dnearneigh(coords, d1=0, d2=25, longlat = TRUE) />/nbLocal<-
>>> dnearneigh(coords, d1=-1, d2=25, longlat = TRUE) #both lines /produce
>>> the same output
>>> /summary(nbLocal) /Neighbour list object:
>> Number of regions: 3
>> Number of nonzero links: 4
>> Percentage nonzero weights: 44.44444
>> Average number of links: 1.333333
>> Link number distribution:
>>
>> 1 2
>> 2 1
>> 2 least connected regions:
>> 1 2 with 1 link
>> 1 most connected region:
>> 3 with 2 links
>>> //
>> Thanks
>> Maël
>>
>>
>>     [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

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Re: dnearneigh() from spdep: Points with the exact same location are not considered neighbours.

Roger Bivand
Administrator
On Wed, 12 Apr 2017, Maël Le Noc wrote:

> Dear Roger,
> Thank you for your answer, (And sorry for the HTML posting).
>
> The issue persists if I specify "GE" for the lower bound, but only when
> the parameter latlong is set to TRUE (see example below).

Thanks, very useful. The Great Circle distance measure returned NotANumber
for zero distance, because of an unprotected division by zero. I've
committed a patched source version to R-Forge. Look on

https://r-forge.r-project.org/R/?group_id=182

later today for a version with today's date and Rev: 693 - should show up
mid to late evening CEST. Please say whether this performs as expected.

>
>
> Regarding the nature of my data, it is a series of record of Jews
> arrested during the Holocaust in Italy. Those are point data, and some
> people have been arrested at the same place and at the same time (hence
> my problem). I am trying to assess spatial autocorrelation for a binary
> attribute (whether they survived the Holocaust or not), and I plan to
> use a Join-count method, for which I need a spatial weight matrix. Is
> using Join-count on such a dataset wrong ?

Join-count should be OK, but if you have covariates you could try to
remove the mean model first and only then see whether there is a spatially
structured random effect, for example with hglm, R2BayesX, INLA, or
similar. For hglm see for example:

https://journal.r-project.org/archive/2015/RJ-2015-017/index.html

The data you most likely do not have (addresses with residents at
risk of arrest but not arrested) would also help, giving you a risk of
arrest measure by address. There is also a spatial probit literature that
might be relevant; if you have timestamps, you will likely find that
operational factors play in, with arrests in a small area at the same
time.

Hope this helps,

Roger

>
> Best
>
>
>
> Code:
>
> library(data.table)
> library(spdep)
> pointstable <- data.table(XCoord=c(13.667029,13.667029,13.667028),
> YCoord=c(42.772396,42.772396,42.772396))
> print(pointstable)
> coords <-cbind(pointstable$XCoord, pointstable$YCoord)
> nbLocal<- dnearneigh(coords, d1=0, d2=25, longlat = TRUE, bound =
> c("GE", "LE"))
> summary(nbLocal)
> nbLocal<- dnearneigh(coords, d1=0, d2=25, longlat = FALSE, bound =
> c("GE", "LE"))
> summary(nbLocal)
>
>
> Output:
>> print(pointstable)
>     XCoord  YCoord
> 1: 13.66703 42.7724
> 2: 13.66703 42.7724
> 3: 13.66703 42.7724
>
>> nbLocal<- dnearneigh(coords, d1=0, d2=25, longlat = TRUE, bound =
> c("GE", "LE"))
>> summary(nbLocal)
> Neighbour list object:
> Number of regions: 3
> Number of nonzero links: 4
> Percentage nonzero weights: 44.44444
> Average number of links: 1.333333
> Link number distribution:
>
> 1 2
> 2 1
> 2 least connected regions:
> 1 2 with 1 link
> 1 most connected region:
> 3 with 2 links
>
>> nbLocal<- dnearneigh(coords, d1=0, d2=25, longlat = FALSE, bound =
> c("GE", "LE"))
>> summary(nbLocal)
> Neighbour list object:
> Number of regions: 3
> Number of nonzero links: 6
> Percentage nonzero weights: 66.66667
> Average number of links: 2
> Link number distribution:
>
> 2
> 3
> 3 least connected regions:
> 1 2 3 with 2 links
> 3 most connected regions:
> 1 2 3 with 2 links
>
>
>
> On 12/04/2017 02:27, Roger Bivand wrote:
>> Do not post HTML-mail, only plain text. Your example is not reproducible
>> because you used HTML-mail.
>>
>> Please read the help file, the bounds are described as being between
>> lower (greater than) and upper (less than or equal to) bounds. Since the
>> distance between identical points is strictly zero, they are not
>> neighbours because the distance must be > d1 and <= d2. If d1 is < 0, it
>> is reset to 0, as it is assumed that a negative lower bound is a user
>> error (and it would break the underlying compiled code).
>>
>> In any case, no reasonable cross-sectional spatial process has
>> duplicated point (nugget) observations in situations in which spatial
>> weights would be used (spatio-temporal panels will have, but then time
>> differs).
>>
>> Hope this clarifies,
>>
>> Roger
>>
>> On Wed, 12 Apr 2017, Maël Le Noc via R-sig-Geo wrote:
>>
>>> Dear List
>>>
>>> As I was working on a project, I realized that when I use dnearneigh
>>> from spdep, two (or more) points that have the exact same coordinates
>>> are not considered neighbours and thus are not linked (even when the
>>> lower bound is put to 0 or even to -1). See below for an example.
>>> (However this does not happen if the parameter longlat is set to false)
>>>
>>> Does the function behave the same way for you? Am I missing something?
>>> Is this an expected behavior? And if so, if there a way to change that ?
>>>
>>> In the example below, points 1 and 2 are not connected to each other/are
>>> not neighbours (as you can see since the both have only one link, to 3),
>>> even though they have the exact same coordinates (and are thus less than
>>> 25km apart), while point 3 is connected to both point 1 and 2.
>>> If I want to assess autocorrelation using, for instance joincount.test,
>>> this is then an issue...
>>>
>>>> /library(data.table) />/library(spdep) />/pointstable <-
>>>> data.table(XCoord=c(13.667029,13.667029,13.667028),
>>>> /YCoord=c(42.772396,42.772396,42.772396))
>>>> /print(pointstable) /     XCoord  YCoord
>>> 1: 13.667029 42.772396
>>> 2: 13.667029 42.772396
>>> 3: 13.667028 42.772396
>>>> /coords <-cbind(pointstable$XCoord, pointstable$YCoord) />/nbLocal<-
>>>> dnearneigh(coords, d1=0, d2=25, longlat = TRUE) />/nbLocal<-
>>>> dnearneigh(coords, d1=-1, d2=25, longlat = TRUE) #both lines /produce
>>>> the same output
>>>> /summary(nbLocal) /Neighbour list object:
>>> Number of regions: 3
>>> Number of nonzero links: 4
>>> Percentage nonzero weights: 44.44444
>>> Average number of links: 1.333333
>>> Link number distribution:
>>>
>>> 1 2
>>> 2 1
>>> 2 least connected regions:
>>> 1 2 with 1 link
>>> 1 most connected region:
>>> 3 with 2 links
>>>> //
>>> Thanks
>>> Maël
>>>
>>>
>>>     [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> [hidden email]
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>
>
--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: [hidden email]
Editor-in-Chief of The R Journal, https://journal.r-project.org/index.html
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
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Re: dnearneigh() from spdep: Points with the exact same location are not considered neighbours.

R-sig-geo mailing list
Thank you Roger,
Your patched version now works as expected!

And thank you for your suggestions, I am currently looking into all of that.
Best
Maël



On 12/04/2017 09:00, Roger Bivand wrote:

> On Wed, 12 Apr 2017, Maël Le Noc wrote:
>
>> Dear Roger,
>> Thank you for your answer, (And sorry for the HTML posting).
>>
>> The issue persists if I specify "GE" for the lower bound, but only when
>> the parameter latlong is set to TRUE (see example below).
>
> Thanks, very useful. The Great Circle distance measure returned
> NotANumber for zero distance, because of an unprotected division by
> zero. I've committed a patched source version to R-Forge. Look on
>
> https://r-forge.r-project.org/R/?group_id=182
>
> later today for a version with today's date and Rev: 693 - should show
> up mid to late evening CEST. Please say whether this performs as
> expected.
>
>>
>>
>> Regarding the nature of my data, it is a series of record of Jews
>> arrested during the Holocaust in Italy. Those are point data, and some
>> people have been arrested at the same place and at the same time (hence
>> my problem). I am trying to assess spatial autocorrelation for a binary
>> attribute (whether they survived the Holocaust or not), and I plan to
>> use a Join-count method, for which I need a spatial weight matrix. Is
>> using Join-count on such a dataset wrong ?
>
> Join-count should be OK, but if you have covariates you could try to
> remove the mean model first and only then see whether there is a
> spatially structured random effect, for example with hglm, R2BayesX,
> INLA, or similar. For hglm see for example:
>
> https://journal.r-project.org/archive/2015/RJ-2015-017/index.html
>
> The data you most likely do not have (addresses with residents at risk
> of arrest but not arrested) would also help, giving you a risk of
> arrest measure by address. There is also a spatial probit literature
> that might be relevant; if you have timestamps, you will likely find
> that operational factors play in, with arrests in a small area at the
> same time.
>
> Hope this helps,
>
> Roger
>
>>
>> Best
>>
>>
>>
>> Code:
>>
>> library(data.table)
>> library(spdep)
>> pointstable <- data.table(XCoord=c(13.667029,13.667029,13.667028),
>> YCoord=c(42.772396,42.772396,42.772396))
>> print(pointstable)
>> coords <-cbind(pointstable$XCoord, pointstable$YCoord)
>> nbLocal<- dnearneigh(coords, d1=0, d2=25, longlat = TRUE, bound =
>> c("GE", "LE"))
>> summary(nbLocal)
>> nbLocal<- dnearneigh(coords, d1=0, d2=25, longlat = FALSE, bound =
>> c("GE", "LE"))
>> summary(nbLocal)
>>
>>
>> Output:
>>> print(pointstable)
>>     XCoord  YCoord
>> 1: 13.66703 42.7724
>> 2: 13.66703 42.7724
>> 3: 13.66703 42.7724
>>
>>> nbLocal<- dnearneigh(coords, d1=0, d2=25, longlat = TRUE, bound =
>> c("GE", "LE"))
>>> summary(nbLocal)
>> Neighbour list object:
>> Number of regions: 3
>> Number of nonzero links: 4
>> Percentage nonzero weights: 44.44444
>> Average number of links: 1.333333
>> Link number distribution:
>>
>> 1 2
>> 2 1
>> 2 least connected regions:
>> 1 2 with 1 link
>> 1 most connected region:
>> 3 with 2 links
>>
>>> nbLocal<- dnearneigh(coords, d1=0, d2=25, longlat = FALSE, bound =
>> c("GE", "LE"))
>>> summary(nbLocal)
>> Neighbour list object:
>> Number of regions: 3
>> Number of nonzero links: 6
>> Percentage nonzero weights: 66.66667
>> Average number of links: 2
>> Link number distribution:
>>
>> 2
>> 3
>> 3 least connected regions:
>> 1 2 3 with 2 links
>> 3 most connected regions:
>> 1 2 3 with 2 links
>>
>>
>>
>> On 12/04/2017 02:27, Roger Bivand wrote:
>>> Do not post HTML-mail, only plain text. Your example is not
>>> reproducible
>>> because you used HTML-mail.
>>>
>>> Please read the help file, the bounds are described as being between
>>> lower (greater than) and upper (less than or equal to) bounds. Since
>>> the
>>> distance between identical points is strictly zero, they are not
>>> neighbours because the distance must be > d1 and <= d2. If d1 is <
>>> 0, it
>>> is reset to 0, as it is assumed that a negative lower bound is a user
>>> error (and it would break the underlying compiled code).
>>>
>>> In any case, no reasonable cross-sectional spatial process has
>>> duplicated point (nugget) observations in situations in which spatial
>>> weights would be used (spatio-temporal panels will have, but then time
>>> differs).
>>>
>>> Hope this clarifies,
>>>
>>> Roger
>>>
>>> On Wed, 12 Apr 2017, Maël Le Noc via R-sig-Geo wrote:
>>>
>>>> Dear List
>>>>
>>>> As I was working on a project, I realized that when I use dnearneigh
>>>> from spdep, two (or more) points that have the exact same coordinates
>>>> are not considered neighbours and thus are not linked (even when the
>>>> lower bound is put to 0 or even to -1). See below for an example.
>>>> (However this does not happen if the parameter longlat is set to
>>>> false)
>>>>
>>>> Does the function behave the same way for you? Am I missing something?
>>>> Is this an expected behavior? And if so, if there a way to change
>>>> that ?
>>>>
>>>> In the example below, points 1 and 2 are not connected to each
>>>> other/are
>>>> not neighbours (as you can see since the both have only one link,
>>>> to 3),
>>>> even though they have the exact same coordinates (and are thus less
>>>> than
>>>> 25km apart), while point 3 is connected to both point 1 and 2.
>>>> If I want to assess autocorrelation using, for instance
>>>> joincount.test,
>>>> this is then an issue...
>>>>
>>>>> /library(data.table) />/library(spdep) />/pointstable <-
>>>>> data.table(XCoord=c(13.667029,13.667029,13.667028),
>>>>> /YCoord=c(42.772396,42.772396,42.772396))
>>>>> /print(pointstable) /     XCoord  YCoord
>>>> 1: 13.667029 42.772396
>>>> 2: 13.667029 42.772396
>>>> 3: 13.667028 42.772396
>>>>> /coords <-cbind(pointstable$XCoord, pointstable$YCoord) />/nbLocal<-
>>>>> dnearneigh(coords, d1=0, d2=25, longlat = TRUE) />/nbLocal<-
>>>>> dnearneigh(coords, d1=-1, d2=25, longlat = TRUE) #both lines /produce
>>>>> the same output
>>>>> /summary(nbLocal) /Neighbour list object:
>>>> Number of regions: 3
>>>> Number of nonzero links: 4
>>>> Percentage nonzero weights: 44.44444
>>>> Average number of links: 1.333333
>>>> Link number distribution:
>>>>
>>>> 1 2
>>>> 2 1
>>>> 2 least connected regions:
>>>> 1 2 with 1 link
>>>> 1 most connected region:
>>>> 3 with 2 links
>>>>> //
>>>> Thanks
>>>> Maël
>>>>
>>>>
>>>>     [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
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