README.md

In wpeterman/ResistanceOptimization: Optimizes continuous resistance surfaces using CIRCUITSCAPE v4.0 or greater

ResistanceOptimization

THIS PACKAGE IS NO LONGER BEING UPDATED OR SUPPORTED!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!

wpeterman/ResistanceOptimization documentation built on May 4, 2019, 9:48 a.m.