I am currently looking into circuit theory resistance modelling (http://goo.gl/fPOSVw) as an alternative to least-cost path approaches for modelling ecological connectivity throughout a major surface water network in Australia.
The Circuitscape (http://www.circuitscape.org/) software package seems to do everything I would like to do, but ideally I would prefer to conduct my analyses completely within the R environment. The "commuteDistance" function within the "gdistance" R package (http://cran.r-project.org/web/packages/gdistance/) comes close, but seems to only support resistance modelling between points/nodes, rather than two-dimensional patches/polygons as is possible in Circuitscape.
Is anyone aware of an R package which allows for circuit theory resistance distance modelling between patches, or an alternative approach I could use to achieve similar results?
From my understanding it's pretty easy to call Circuitscape from R. All you need to do is create the .ini files and then call cs_run.exe, which is located in the installation directory. We do that in Python, and I know others (Bill Peterman, who is in the Circuitscape user group comes to mind) do it using R. Note that we will be releasing a completely overhauled version (4.0) in the next 2 weeks (there's a beta version on GitHub if you want to see it sooner) that runs about 2.5 times faster and solves grids that are 4-5x larger. Hope this helps.
The authors of this paper uses Circuit Theory in R, but I think they wrote their own function. You can perhaps contact them
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047141#pone.0047141-Csardi1
There are system tools in R that allow you to call python packages (I think circuitcape is one? See last post in this thread?
https://groups.google.com/forum/#!topic/circuitscape/klY0O01RGJA
From my understanding it's pretty easy to call Circuitscape from R. All you need to do is create the .ini files and then call cs_run.exe, which is located in the installation directory. We do that in Python, and I know others (Bill Peterman, who is in the Circuitscape user group comes to mind) do it using R. Note that we will be releasing a completely overhauled version (4.0) in the next 2 weeks (there's a beta version on GitHub if you want to see it sooner) that runs about 2.5 times faster and solves grids that are 4-5x larger. Hope this helps.
I'm away from my work computer until Tuesday, but if you want to dig into a roughly built R package, here is a link to my GitHub project:
https://github.com/wpeterman/ResistanceOptimization
And the paper that describes its use:
https://www.researchgate.net/publication/261477066_Ecological_resistance_surfaces_predict_fine_scale_genetic_differentiation_in_a_terrestrial_woodland_salamander?ev=prf_pub
In the package there are functions to write .ini files, call Circuitscape, and import results back into R. I can pass along the relevant components next week if I get a better idea of what you're looking for.
Article Ecological resistance surfaces predict fine scale genetic di...
Here is a function to run CS from R on Linux: https://github.com/rojaff/runCS
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