spdep: show neighbors from "dnearneigh"

I am having trouble viewing the list of neighbors ("regions IDs") after
created a nb object using the "dnearneigh" function in spdep.  I only seem
to get a summary (with # regions, # non-zero links, etc.).  This nb object
also doesn't take well to being converted to another type of object, or
exported from R.  How I view the list of neighbors?

nb

Wmat <- nb2mat(nb, style="W")

lw <- nb2listw(nb, style="W")
spWmat <- as(as_dgRMatrix_listw(lw), "CsparseMatrix")

Some additional background: I'm identifying all neighboring bird nests
within 100m of each nest.  For this particular analysis, I ultimately want
to calculate the average vegetation height of neighboring nests to compare
with the focal nest.  This will involve generating a list of neighbors, and
merging that list with my other data.

class(nb) <- NULL

attr(nb, "region.id")

Thanks,

Kevin


	[[alternative HTML version deleted]]

I am having trouble viewing the list of neighbors ("regions IDs") after
created a nb object using the "dnearneigh" function in spdep.  I only seem
to get a summary (with # regions, # non-zero links, etc.).  This nb object
also doesn't take well to being converted to another type of object, or
exported from R.  How I view the list of neighbors?

nb

Wmat <- nb2mat(nb, style="W")

lw <- nb2listw(nb, style="W")
spWmat <- as(as_dgRMatrix_listw(lw), "CsparseMatrix")

Some additional background: I'm identifying all neighboring bird nests
within 100m of each nest.  For this particular analysis, I ultimately want
to calculate the average vegetation height of neighboring nests to compare
with the focal nest.  This will involve generating a list of neighbors,

merging that list with my other data.

class(nb) <- NULL

attr(nb, "region.id")

Thanks,

Kevin


	[[alternative HTML version deleted]]

Hi,

Maybe you should convert your nb object into a matrix using nb2mat then use
reshape package?

library(reshape)

df<-as.data.frame(nb.mat)

df$id<-row.names(df)

mdata<-melt(df,id="id")

then subset your data for which mdata$value > 0

2011/3/21 Kevin Ringelman <kmringelman at ucdavis.edu>

Thanks for your help Roger.  I have a couple more questions.

print.default(nb) shows me what I'm looking for: for each region, I see the
regions that are within my distance band.  For example:

[[1]]
 [1]   2  10  11  15  17  18  19  32  40 554

[[2]]
 [1]   1  15  17  21  33  34 426 511 554 557

I want to make this information into a table, with the focal regions as
column 1, and the region IDs of it's neighbors as column 2 (similar to
neighbor analysis output in ArcGIS).  Continuing the example from above:
1       2
1       10
1       11
1       15
1       17
(etc.)

Even after I nuke the nb class
U <- unclass(nb)
I still can't access or manipulate the data...it doesn't appear as an
attribute
attribute(U)

Any suggestions?





-----Original Message-----
From: Roger Bivand [mailto:Roger.Bivand at nhh.no]
Sent: Saturday, March 05, 2011 10:03 AM
To: Kevin Ringelman
Cc: r-sig-geo at r-project.org
Subject: Re: [R-sig-Geo] spdep: show neighbors from "dnearneigh"

On Fri, 4 Mar 2011, Kevin Ringelman wrote:

I am having trouble viewing the list of neighbors ("regions IDs") after
created a nb object using the "dnearneigh" function in spdep.  I only

seem

to get a summary (with # regions, # non-zero links, etc.).  This nb

object

also doesn't take well to being converted to another type of object, or
exported from R.  How I view the list of neighbors?

In S and R, objects with a class attribute, such as "nb" objects, may have
display methods specific to the class. If you just say:

nb

then this is expanded internally to print(nb), and since nb is an object
of class "nb", the print.nb() method is chosen. If you want the default
print method, call it as print.default(nb). Conversion of objects of one
class to another class may be done by coercion where coercion methods are
provided. No such methods are available for nb objects. There are
functions to do things like this, but not methods. For example, to make an
nb object into a row-standardised matrix, you might do:

Wmat <- nb2mat(nb, style="W")

but you should avoid this if your number of observations is large. To make
a sparse matrix, several steps are required:

lw <- nb2listw(nb, style="W")
spWmat <- as(as_dgRMatrix_listw(lw), "CsparseMatrix")

using the nb2listw() and (ugly name) as_dgRMatrix_listw() functions, and
coercion from one representation to another using new-style classes
defined in the Matrix package.

Some additional background: I'm identifying all neighboring bird nests
within 100m of each nest.  For this particular analysis, I ultimately

want

to calculate the average vegetation height of neighboring nests to

compare

with the focal nest.  This will involve generating a list of neighbors,

and

merging that list with my other data.

Note that an nb object is a list - to nuke the class, do:

class(nb) <- NULL

which lets you call print.default(), but to get at the attribute you want,
just do:

attr(nb, "region.id")

to call print.default on the character vector it contains.

Hope this clarifies,

Roger

Thanks,

Kevin


      [[alternative HTML version deleted]]

--
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

	[[alternative HTML version deleted]]

Hi,

Maybe you should convert your nb object into a matrix using nb2mat then

reshape package?

library(reshape)

df<-as.data.frame(nb.mat)

df$id<-row.names(df)

mdata<-melt(df,id="id")

then subset your data for which mdata$value > 0

2011/3/21 Kevin Ringelman <kmringelman at ucdavis.edu>

Thanks for your help Roger.  I have a couple more questions.

print.default(nb) shows me what I'm looking for: for each region, I see

regions that are within my distance band.  For example:

[[1]]
 [1]   2  10  11  15  17  18  19  32  40 554

[[2]]
 [1]   1  15  17  21  33  34 426 511 554 557

I want to make this information into a table, with the focal regions as
column 1, and the region IDs of it's neighbors as column 2 (similar to
neighbor analysis output in ArcGIS).  Continuing the example from above:
1       2
1       10
1       11
1       15
1       17
(etc.)

Even after I nuke the nb class
U <- unclass(nb)
I still can't access or manipulate the data...it doesn't appear as an
attribute
attribute(U)

Any suggestions?





-----Original Message-----
From: Roger Bivand [mailto:Roger.Bivand at nhh.no]
Sent: Saturday, March 05, 2011 10:03 AM
To: Kevin Ringelman
Cc: r-sig-geo at r-project.org
Subject: Re: [R-sig-Geo] spdep: show neighbors from "dnearneigh"

On Fri, 4 Mar 2011, Kevin Ringelman wrote:

I am having trouble viewing the list of neighbors ("regions IDs") after
created a nb object using the "dnearneigh" function in spdep.  I only

seem

to get a summary (with # regions, # non-zero links, etc.).  This nb

object

also doesn't take well to being converted to another type of object, or
exported from R.  How I view the list of neighbors?

In S and R, objects with a class attribute, such as "nb" objects, may

display methods specific to the class. If you just say:

nb

then this is expanded internally to print(nb), and since nb is an object
of class "nb", the print.nb() method is chosen. If you want the default
print method, call it as print.default(nb). Conversion of objects of one
class to another class may be done by coercion where coercion methods are
provided. No such methods are available for nb objects. There are
functions to do things like this, but not methods. For example, to make

nb object into a row-standardised matrix, you might do:

Wmat <- nb2mat(nb, style="W")

but you should avoid this if your number of observations is large. To

a sparse matrix, several steps are required:

lw <- nb2listw(nb, style="W")
spWmat <- as(as_dgRMatrix_listw(lw), "CsparseMatrix")

using the nb2listw() and (ugly name) as_dgRMatrix_listw() functions, and
coercion from one representation to another using new-style classes
defined in the Matrix package.

Some additional background: I'm identifying all neighboring bird nests
within 100m of each nest.  For this particular analysis, I ultimately

want

to calculate the average vegetation height of neighboring nests to

compare

with the focal nest.  This will involve generating a list of neighbors,

and

merging that list with my other data.

Note that an nb object is a list - to nuke the class, do:

class(nb) <- NULL

which lets you call print.default(), but to get at the attribute you

just do:

attr(nb, "region.id")

to call print.default on the character vector it contains.

Hope this clarifies,

Roger

Thanks,

Kevin


      [[alternative HTML version deleted]]

--
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

	[[alternative HTML version deleted]]

Thanks Roger and Mathieu.  Instead of:
[[1]]
 [1]   2  10  11  15  17

I now have:
1	2
1	10
1	11
1	15
1	17

For the last piece of this analysis, I would like to generate a list of
neighbor distances to complete my table.
nbd <- nbdist(nb, SpatialPoints)
nbd
[[1]]
[1] 84.95881 90.35486 75.92760 22.20360 81.00617

But ideally, I would like to have
1	2	84.95881
1	10	90.35486
1	11	75.92760
1	15	22.20360
1	17	81.00617

I can't use nb2listw (and then merge), because this is an object of class
"nbdist".  I also cannot use the Mathieu's melt method, because I nb2mat
also requires an object of class "nb".

Suggestions?




-----Original Message-----
From: Roger Bivand [mailto:Roger.Bivand at nhh.no]
Sent: Tuesday, March 22, 2011 1:30 AM
To: Mathieu Rajerison
Cc: kmringelman at ucdavis.edu; r-sig-geo at r-project.org
Subject: Re: [R-sig-Geo] spdep: show neighbors from "dnearneigh"

On Tue, 22 Mar 2011, Mathieu Rajerison wrote:

Hi,

Maybe you should convert your nb object into a matrix using nb2mat then

use

reshape package?

library(reshape)

df<-as.data.frame(nb.mat)

df$id<-row.names(df)

mdata<-melt(df,id="id")

then subset your data for which mdata$value > 0

No, the question was how to convert to a two-column from-to
representation, and a direct route is:

example(read.gal)
# to get an nb object
us48.q
us48.q[1:2]
res <- listw2sn(nb2listw(us48.q))[,1:2]
res[1:9,]
str(res)

If you need a matrix, do as.matrix(res).

Roger

2011/3/21 Kevin Ringelman <kmringelman at ucdavis.edu>

Thanks for your help Roger.  I have a couple more questions.

print.default(nb) shows me what I'm looking for: for each region, I see

the

regions that are within my distance band.  For example:

[[1]]
 [1]   2  10  11  15  17  18  19  32  40 554

[[2]]
 [1]   1  15  17  21  33  34 426 511 554 557

I want to make this information into a table, with the focal regions as
column 1, and the region IDs of it's neighbors as column 2 (similar to
neighbor analysis output in ArcGIS).  Continuing the example from above:
1       2
1       10
1       11
1       15
1       17
(etc.)

Even after I nuke the nb class
U <- unclass(nb)
I still can't access or manipulate the data...it doesn't appear as an
attribute
attribute(U)

Any suggestions?





-----Original Message-----
From: Roger Bivand [mailto:Roger.Bivand at nhh.no]
Sent: Saturday, March 05, 2011 10:03 AM
To: Kevin Ringelman
Cc: r-sig-geo at r-project.org
Subject: Re: [R-sig-Geo] spdep: show neighbors from "dnearneigh"

On Fri, 4 Mar 2011, Kevin Ringelman wrote:

I am having trouble viewing the list of neighbors ("regions IDs") after
created a nb object using the "dnearneigh" function in spdep.  I only

seem

to get a summary (with # regions, # non-zero links, etc.).  This nb

object

also doesn't take well to being converted to another type of object, or
exported from R.  How I view the list of neighbors?

In S and R, objects with a class attribute, such as "nb" objects, may

have

display methods specific to the class. If you just say:

nb

then this is expanded internally to print(nb), and since nb is an object
of class "nb", the print.nb() method is chosen. If you want the default
print method, call it as print.default(nb). Conversion of objects of one
class to another class may be done by coercion where coercion methods are
provided. No such methods are available for nb objects. There are
functions to do things like this, but not methods. For example, to make

an

nb object into a row-standardised matrix, you might do:

Wmat <- nb2mat(nb, style="W")

but you should avoid this if your number of observations is large. To

make

a sparse matrix, several steps are required:

lw <- nb2listw(nb, style="W")
spWmat <- as(as_dgRMatrix_listw(lw), "CsparseMatrix")

using the nb2listw() and (ugly name) as_dgRMatrix_listw() functions, and
coercion from one representation to another using new-style classes
defined in the Matrix package.

Some additional background: I'm identifying all neighboring bird nests
within 100m of each nest.  For this particular analysis, I ultimately

want

to calculate the average vegetation height of neighboring nests to

compare

with the focal nest.  This will involve generating a list of neighbors,

and

merging that list with my other data.

Note that an nb object is a list - to nuke the class, do:

class(nb) <- NULL

which lets you call print.default(), but to get at the attribute you

want,

just do:

attr(nb, "region.id")

to call print.default on the character vector it contains.

Hope this clarifies,

Roger

Thanks,

Kevin


      [[alternative HTML version deleted]]

--
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

	[[alternative HTML version deleted]]