[R-sig-Geo] Computing pairwise minimum distance moving only within clipped area

Ege Rubak rub@k @end|ng |rom m@th@@@u@dk
Tue Oct 15 12:01:20 CEST 2019

 From the documentation of gDistance I would be very suprised if it 
confines paths to be inside the polygon. Try to make a simple example 
"by hand" and check the calculations.

This is a well studied problem in computer science (search for something 
like "shortest path inside polygon"), and different algorithms to solve 
the problem exist, but I don't know if any of them are implemented in R.

A grid based approach which may be the simplest/best solution for you is 
described in this answer on StackOverflow:


Hope this helps,

On 12/10/2019 21.37, Carrie Perkins wrote:
> Hello!
> I am trying to compute pairwise minimum distances within a raster that has
> been clipped to an outer boundary using a polygon.
> I tried to do this using gDistance (reproducible example below) but am not
> sure if it worked. I need to know the pairwise distances between patches
> where the path travelled does not exit the clipped boundary (in the example
> below, this is the border of Switzerland).
> library(maptools)
> library(raster)
> data(wrld_simpl)
> SPDF <- subset(wrld_simpl, NAME=="Switzerland") #polygon map of Switzerland
> ## Example RasterLayer
> r <- raster(nrow=1000, ncol=1000, crs=proj4string(SPDF)) #blank raster
> r[] <- 0 #set all cell values in raster to 0
> ## crop raster to extent of Switzerland polygon, SPDF
> r2 <- crop(r, extent(SPDF))
> #create patches by setting certain cells in raster to value 1; all other
> cells are still 0
> r2[8,1] <- 1
> r2[9,11] <- 1
> plot(r2)
> p <- clump(r3) #give each patch of its own unique ID
> spplot(p)
> p[is.na(p[])] <- 0 #all cells that were previously 0 were set to NA by
> clump() so we need to change them back to 0
> p.masked <- mask(p,SPDF) #now clip the raster to the border of Switzerland
> using SPDF; outside of Switzerland's border cells are now NA
> plot(p.masked)
> rpoly <- rasterToPolygons(p.masked, dissolve=T) #convert from raster to
> polygons; NA cells (outside Switzerland) do not get converted
> d <- gDistance(rpoly, byid=T) #calculate minimum pairwise distances between
> polygons
> library(reshape2)
> df <- melt(as.matrix(d), varnames = c("row", "col")) #put pairwise
> distances into a dataframe
> #add column names
> colnames(df) <- c("node_i_ID","node_j_ID","Distance")
> df
> I cannot tell whether gDistance did what I am trying to do, i.e. calculate
> the minimum pairwise distances among patches without leaving the boundary
> of Switzerland, or whether the path travelled includes areas outside of
> Switzerland. If it is the latter, I could use some help figuring out a way
> to keep the path travelled confined to the country boundary. Thanks!
> 	[[alternative HTML version deleted]]
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