[R-sig-Geo] adding links to neighbour lists

[Roger Bivand]

On Mon, 12 Jun 2006, Steven J. Pierce wrote:

> Hi folks,
> 
> I tried Roger's suggested method for adding extra links directly into a
> neighbor list. To get it to work, I had to coerce the vector representing
> the new link to be an integer vector instead of a numeric vector. Here's
> what worked.

Yes, of course, thanks for your careful attention! 

Roger

> 
> # Create an integer vector of the 2 regions (23 & 31) that need to be
> connected.
> 
> ij <- as.integer(c(23,31))
> 
> # Update the neighbor list to add the symmetric link.
> 
> nb[[ij[1]]] <- sort(unique(c(nb[[ij[1]]], ij[2])))
> nb[[ij[2]]] <- sort(unique(c(nb[[ij[2]]], ij[1])))
> 
> I just wanted to share that detail back to the list in case anyone else
> wants to do this sort of data manipulation.
> 
> Steven J. Pierce
> E-mail: pierces1 at msu.edu
> 
> -----Original Message-----
> From: Roger Bivand [mailto:Roger.Bivand at nhh.no] 
> Sent: Saturday, June 03, 2006 7:11 AM
> To: Steven J. Pierce
> Cc: r-sig-geo at stat.math.ethz.ch
> Subject: Re: [R-sig-Geo] adding links to neighbour lists
> 
> On Fri, 2 Jun 2006, Steven J. Pierce wrote:
> 
> > Hi folks,
> > 
> > After using spdep to construct a neighbor list from a SpatialPolygons
> > object, I plotted the neighbor list and noted that I needed one more link
> > that wasn't caught by the poly2nb command. I found the edit.nb() function
> > and can successfully use the interactive graphical interface to add the
> > link, but would like to know if there is an alternative method for adding
> a
> > link between two regions. What would I need to do to directly edit the
> > neighbor list object to include an additional link between regions 23 and
> > 31?
> 
> There is a drop.links() function but no add.links(). So yes, you could 
> manipulate the list directly. If ij is a two element vector for the 
> missing link:
> 
> nb[[ij[1]]] <- sort(unique(c(nb[[ij[1]]], ij[2])))
> nb[[ij[2]]] <- sort(unique(c(nb[[ij[2]]], ij[1])))
> 
> should do it (untried). If there are more links, have a look at drop.links 
> and see if you can adapt it.
> 
> > 
> > 
> > > # Create a SpatialPolygons object from a SpatialPolygonsDataFrame
> object,
> > this
> > > # helps set up for creating a neighbor list via commands from spdep
> > package
> > > 
> > > CITY.polys <- as.SpatialPolygons.PolygonsList(CITY.ZCTA.data at polygons, 
> > +
> > proj4string=CRS(projection.details))
> > > 
> 
> I think:
> 
> CITY.polys <- as(CITY.ZCTA.data, "SpatialPolygons")
> 
> should be enough, in time poly2nb() will do that internally.
> 
> > > # Create a neighbor list based on shared boundary. We need this to
> > facilitate
> > > # creating a weights matrix when we go to do spatial regression models.
> > > 
> > > CITY.nb <- poly2nb(CITY.polys, row.names = NULL,
> > snap=sqrt(.Machine$double.eps), queen=TRUE)
> > > 
> > > # Capture coordinates of ZCTA centroids into a matrix we can use in
> > plotting
> > > # the neighbor list.
> > > 
> > > coords.mat <- cbind(CITY.ZCTA.data$centroid.x,
> CITY.ZCTA.data$centroid.y)
> > > 
> 
> Could be:
> 
> coords.mat <- coordinates(CITY.ZCTA.data)
> 
> if the centroid.x|y values correspond to the polygon centroids.
> 
> Roger
> 
> > > # Plot the neighbor list (reveals we need to add 1 more link)
> > > 
> > > plot(CITY.ZCTA.data, col="grey", border="black", axes=FALSE, asp=1,
> > yaxs="i")
> > > title(main="Neighbor List Links", adj= 0, cex.sub=.75)
> > > plot(CITY.nb, coords.mat, add=TRUE, col="black", lwd=2)
> > > 
> > > # Add 1 link to neighbor list. This requires interaction with the
> graphics
> > > # on screen.
> > > 
> > > CITY.nb <- edit.nb(CITY.nb, coords.mat, polys=CITY.polys)
> > Identifying contiguity for deletion ...
> > No contiguity between chosen points
> > Add contiguity? (y/n) y
> > added contiguity between point 23 and 31 
> > Options: quit[q] refresh[r] continue[c] q
> > > 
> > > # Plot the revised neighbor list (now everything looks right)
> > > 
> > > plot(CITY.ZCTA.data, col="grey", border="black", axes=FALSE, asp=1,
> > yaxs="i")
> > > title(main="Neighbor List Links", adj= 0, cex.sub=.75)
> > > plot(CITY.nb, coords.mat, add=TRUE, col="black", lwd=2)
> > 
> > 
> > Steven J. Pierce
> > E-mail: pierces1 at msu.edu
> > 
> > _______________________________________________
> > R-sig-Geo mailing list
> > R-sig-Geo at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> > 
> 
> 

-- 
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