c_Section 6 (adjacency matrix)

install.packages(c( "sf", "NipponMap", "spdep" ) )
library( sf ); library( NipponMap ); library( spdep)

##### Read prefecture polygons in Japan
shp   	<- system.file("shapes/jpn.shp", package = "NipponMap")[1]
pref0 	<- read_sf(shp) 
pref0b	<- pref0[pref0$name != "Okinawa",]
st_crs(pref0b) <- 4326	#Specify the EPSG code of WGS84

pref<-st_transform(pref0b,crs=6677)# Specify the EPSG code (Plane Rectangular Coordinates system 9)

##### Neighbors (Queen)
nb1     <- poly2nb(pref)
nb1

coords<- st_coordinates(st_centroid(pref))
plot(st_geometry(pref), col="white", border="grey")
plot(nb1, coords, add=TRUE, col="red",cex=0.01,lwd=1.5)

##### Neighbors (4-nearet neighbors)
knn   <- knearneigh(coords,4)
nb2   <- knn2nb(knn)
plot(st_geometry(pref), border="grey")
plot(nb2, coords, add = TRUE, col="red",cex=0.01,lwd=1.5)

##### Neighbors (8-nearet neighbors)
nb3<-knn2nb(knearneigh(coords,8))
plot(st_geometry(pref), border="grey")
plot(nb3, coords,add = TRUE, col="red",cex=0.01,lwd=1.5)

##### Neighbors (distance-based; equal or less than 150 km)
nb4<-dnearneigh(coords,d1=0, d2= 150000)
plot(st_geometry(pref), border="grey")
plot(nb4, coords,add = TRUE, col="red",cex=0.01,lwd=1.5)

##### Ajacency matrix (nb3)
w3    <-nb2listw(nb3)
w3mat <-listw2mat(w3) 
w3mat[1:5,1:5]

##### Neighbors (distance-decaying function)
nb5   	<- dnearneigh(coords,d1=0, d2= 500000)
glist 	<- nbdists(nb5, coords)
glist 	<- lapply(glist, function(x) 1/x)
w5    	<- nb2listw(nb5, glist = glist)

##### Ajacency matrix (nb5)
w5mat 	<- listw2mat(w5)
w5mat[1:5,1:5]