THIS PACKAGE IS NO LONGER BEING UPDATED OR SUPPORTED! THE METHODS USED IN THIS PACKAGE HAVE BEEN ADDED TO ResistanceGA, AN R PACKAGE THAT USES GENETIC ALGORITHMS TO OPTIMIZE CONTINUOUS AND CATEGORICAL SURFACES, AS WELL AS OPTIMIZE MULTIPLE RESISTANCE SURFACES SIMULTANEOUSLY. ResistanceGA can be found here
R package to optimize continuous resistance surfaces
To install this package, execute the following commands in R:
install.packages("devtools") # Installs the 'devtools' package
library(devtools) # Loads devtools
install_github("wpeterman/ResistanceOptimization") # Downloads package
require(ResistanceOptimization) # Installs package and the other required packages needed
########################################### In order to use this package, you must have CIRCUITSCAPE installed. The 4.0 release is required: Official releases: https://code.google.com/p/circuitscape/downloads/list
You can download example data by going to: https://github.com/wpeterman/ResistanceOptimization/tree/master/data
Right click on ‘Example.zip’, 'Save link as...' to download the .zip file. Extract the zip file.
If all files are extracted to a folder called 'Example' located at 'C:/Example/', and the Circuitscape executable file (cs_run.exe) is located in '"C:/Program Files/Circuitscape/cs_run.exe"', the following lines of code would execute the functions. ############################################
Example.dir <- "C:/Example/"
# Prepare data for optimization function
Optim.input <-Optim.prep(
Response=read.csv(paste0(Example.dir,"RESPONSE_mat.csv"),header=F),
n.Pops=64,
ASCII.dir=Example.dir,
CS_Point.File=paste0(Example.dir,"samples64.txt"),
CS.exe='"C:/Program Files/Circuitscape/cs_run.exe"',
Neighbor.Connect=8,
Constrained.Max=100,
Initial.shape=c(seq(0.1,1,0.4),seq(1.5,10,1.5)),
Bootstrap=TRUE,
boot.iters=10000,
Sample_Proportion=0.75)
# Run optimization function
Resistance.Optimization(Optim.input=Optim.input)
# Create Diagnostic plots
Diagnostic.Plots(resist.matrix.path=paste0(Optim.input$Results.dir,"Final_CS_Surfaces/Resist_surf1_resistances.out
"),
genetic.dist.vec=Optim.input$Response.vec,
XLAB="Transformed resistance",
YLAB="Pairwise distance",
plot.dir=paste0(Optim.input$Results.dir,"Plots/"))
Further details of of how this method has been implemented can be found in:
Peterman, W. E., G. M. Connette, R. D. Semlitsch, and L. S. Eggert. in press. Ecological resistance surfaces predict fine scale genetic differentiation in a terrestrial woodland salamander. Molecular Ecology:10.1111/mec.12747.
Please cite this paper if you use this method!