On Mon, 21 Jun 2010, Nikhil Kaza wrote:
While answering a question on R-help, I was monkeying with the code in
cell2nb in spdep (5.11) to see if it can be made faster.
Getting rid of the for loop and replacing with lapply and apply only
marginally improves the performance
n <- nrow*ncol
for (i in 1:n) {
res[[i]] <- sort(mrc2vi(xcell(vi2mrc(i, nrow, ncol),
nrow, ncol, torus), nrow, ncol))
rownames[i] <- paste(vi2mrc(i, nrow, ncol), collapse = ":")
}
However, I do not understand why the loop has to run through 1:n. If the
adjacency matrix is symmertic, should we not just make ceil[n/2] comparisons
and take advantage of its symmetry? Am I missing something? Not sure if it
makes it any faster though.
The reason why cell2nb() was written was originally to provide a way of
generating neighbours for grids on a torus, which is hard to do for
coordinates of a planar grid. These are typically needed to simulate
processes without edge effects, for modest grid sizes. Agreed, neighbours
in grids are symmetric, but an "nb" object contains both symmetric links
for generality (the "neig" class in ade4 does not), so these would have to
be added in afterwards. Typically, dnearneigh() with the step distance as
its threshold generates rook neighbours in acceptable time, with the
diagonal distance it yields queen neighbours:
library(spdep)
system.time(res <- cell2nb(10, 10))
user system elapsed
0.099 0.000 0.099
system.time({grd <- GridTopology(c(0,0), c(1,1), c(10,10));
+ resd <- dnearneigh(coordinates(grd), 0, 1)})
user system elapsed
0.003 0.000 0.002
all.equal(res, resd, check.attributes=FALSE)
[1] TRUE
system.time(res <- cell2nb(50, 50)) user system elapsed
2.404 0.001 2.407
system.time({grd <- GridTopology(c(0,0), c(1,1), c(50,50));
+ resd <- dnearneigh(coordinates(grd), 0, 1)})
user system elapsed
0.267 0.000 0.267
all.equal(res, resd, check.attributes=FALSE)[1] TRUE
system.time(res <- cell2nb(100, 100)) user system elapsed
9.817 0.003 9.872
system.time({grd <- GridTopology(c(0,0), c(1,1), c(100,100));
+ resd <- dnearneigh(coordinates(grd), 0, 1)})
user system elapsed
4.125 0.001 4.127
all.equal(res, resd, check.attributes=FALSE)[1] TRUE
It degrades but not as fast, and may be speeded up using rgeos soon (using
a spatial index on the points to cherry-pick, rather than brute-force as
now).
Roger
Nikhil Kaza
Asst. Professor,
City and Regional Planning
University of North Carolina
nikhil.l...@gmail.com
_______________________________________________
R-sig-Geo mailing list
R-sig-Geo@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.biv...@nhh.no
_______________________________________________
R-sig-Geo mailing list
R-sig-Geo@stat.math.ethz.ch
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
