I've also found the below related question very useful, but so far the best non-R or Python tools I've found are either for older software (i.e. Pathmatrix) or don't seem to be capable of processing least-cost paths on the size of my datasets (i.e. Graphab). 

https://www.researchgate.net/post/What_is_the_best_GIS_tool_to_calculate_habitat_connectivity_in_the_landscape

Hi Robbi, have you tried gDistance in rgeos R package? That works with polygons, only I'm not sure if it calculates costs. Otherwise you can rasterize your vector map, and do it in raster using gdistance package (if you calculate the minimum distance between two cluster of cells, you should get a similar result than with vectors). Hope it helps

Hi Luca, thanks for the reply. I've previously used 'gDistance' to calculate euclidean distances between polygons; from what I can tell there doesn't seem to be anything within the rgeos package to allow least-cost path calculations. Rasterising the vector map should be fine, but the best function available in the gdistance package looks like 'costDistance', which I've previously found only works (I believe) with point/coordinate inputs. I may be missing something, however!

costDistance: Cost distance (least-cost distance)

Description: Calculate the least-cost distance between points.

Usage: costDistance(x, fromCoords, toCoords)

http://cran.r-project.org/web/packages/gdistance/gdistance.pdf

Hi Robbi, I've just checked some old codes, I've used gridDistance to create a cost distance map from a patch of a landscape, the patch from which you calculate the distance should be a cluster of cell having the same value (patch_value below)

distmap

Robbi, I'm assuming that these polygons are irregular in shape and spatial distribution to each other, yes? If not, and they are essentially on a predictable grid, then you could convert the polygons to points and run the analysis with gdistance. Another (less attractive) option would be to fill the polygons with many points, write a loop, and run gdistance many times--selecting a different point with each polygon to use each time for your cost analysis. Ugly, but it should work.

Hi Robbi,

There are tool boxes in QGIS and ARCGIS that do this automatically. Try Patch analyst also.

Best,

Guy