polygon neighbor matrix

I second the `gTouches` suggestion. There's a ref here:
http://stackoverflow.com/a/26499134/1457051 but the gist of it is
(this user needed adjacent polygons in ghana):
If this answered the question, it would be OK. But it doesn't, as reading 
the link provided to the FlexScan documentation showed (not a matrix, 
but a ragged right-edged text array).

Using gTouches can work, especially if the returnDense=FALSE argument is 
used (ie. don't return a matrix), but can fail if snapping is needed. 
spdep::poly2nb is the preferred route, because it makes snapping possible, 
and because the nb S3 class is much more flexible than matrices.

Roger
library(rgeos)
library(rgdal)

# using http://data.biogeo.ucdavis.edu/data/diva/adm/GHA_adm.zip
ghana <- readOGR("GHA_adm", "GHA_adm1")

gTouches(ghana, byid=TRUE)

##       0     1     2     3     4     5     6     7     8     9
## 0 FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE
## 1  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE  TRUE
## 2  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE
## 3  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE
## 4 FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE
## 5 FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE
## 6 FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE
## 7 FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE
## 8 FALSE  TRUE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE
## 9  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE

On Mon, Aug 31, 2015 at 2:19 PM, Roger Bivand <Roger.Bivand at nhh.no> wrote:
On Mon, 31 Aug 2015, Paul Lantos wrote:

Hi,

I'm trying to use the cluster analysis program Flexscan, which I gather is
similar to Satscan but it computes irregular clusters. This program requires
a polygon adjacency matrix (termed a 'matrix definition file'). The example
they provide has a row for every polygon, and for each row every neighboring
polygon is listed in successive columns. So for instance if row 1 / polygon
1 has 3 neighbors there will be three polygons listed in columns 2-4.

I have tried some techniques like the spatial weights matrix tools in
ArcGIS and in Spatstat, but I cannot get the output in this kind of format.
Was wondering if there is some obvious way to do this in R.

The documentation for Flexscan is here:

https://sites.google.com/site/flexscansoftware/download_e/FleXScan%20User%20Guide_e31.pdf?attredirects=0&d=1

Something like:

library(spdep)
example(nc.sids)
out <- sapply(seq(along=ncCR85_nb), function(i) paste(attr(ncCR85_nb,
  "region.id")[i], paste(attr(ncCR85_nb, "region.id")[ncCR85_nb[[i]]],
  collapse=" ")))
writeLines(out, tf)
file.show(tf)

See also:

vignette("nb")

Roger

Thanks for any help,
Paul

_______________________________________
Paul M. Lantos, MD, FIDSA, FAAP, FACP
Departments of Internal Medicine and Pediatrics
 Pediatric Infectious Diseases
 Hospital Medicine Program
Duke University School of Medicine
_______________________________________

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--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 91 00
e-mail: Roger.Bivand at nhh.no

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Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 91 00
e-mail: Roger.Bivand at nhh.no

polygon neighbor matrix

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