Simple script that shows how to run Circuitscape through R under Windows. It runs data created directly in R.

Circuitscape example.R

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####         Example Run          ####
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# Clear workspace
rm(list=ls())

# load raster library
library(raster)

# Make a place holder for the cs_run.exe path
CS_exe <- 'C:/"Program Files"/Circuitscape/cs_run.exe' # Don't forget the "Program Files" problem

# Cost surface
cost <- raster(matrix(abs(rnorm(10000,1000,100)),100,100))

# Locs
sites <- SpatialPoints(cbind(c(0.1,0.9),c(0.1,0.9)))

# Plot it
plot(cost)
points(sites,pch=19,col=2)

# Rasterize points using the cost extent
sites <- rasterize(x = sites,y = cost)

# Write rasters to your working directory
writeRaster(sites,"sites_rast.asc",overwrite=TRUE)
writeRaster(cost,"cost_rast.asc",overwrite=TRUE)

# Make an .ini file
CS_ini <- c("[circuitscape options]",            
            "data_type = raster",
            "scenario = pairwise",
            paste(c("point_file =",
                    "habitat_file =",
                    "output_file ="),
            paste(getwd(),c("sites_rast.asc",
                            "cost_rast.asc",
                            "CS.out"),
                  sep="/")))

# Write it to your working directory
writeLines(CS_ini,"myini.ini")

# Make the CS run cmd
CS_run <- paste(CS_exe, paste(getwd(),"myini.ini",sep="/")) # Make the cmd

# Run the command
system(CS_run)

# Import the effective resistance
rdist <- as.dist(read.csv("CS_resistances.out",sep=" ",row.names=1,header=1))