Optim.prep: Prepare elements for optimization

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

Description

This function prepares and compiles the necessary components to execute subsequent optimization functions, and must be run first. To run the example data, download the data from GitHub (url)

Usage

Optim.prep(Response, n.Pops, ASCII.dir, CS_Point.File, CS.exe, Neighbor.Connect, Constrained.Max, Initial.shape, Bootstrap, boot.iters, Sample_Proportion)

Arguments

Response	This must be a square distance matrix without row or column names
n.Pops	The number of populations in your study
ASCII.dir	The directory containing the continuous ASCII (.asc) files to be optimized. It is recommended that these files be stored their own directory.
CS_Point.File	The path to the Circuitscape formatted point file. See Circuitscape documentation for help.
CS.exe	The path to the CIRCUITSCAPE executable file (cs_run.exe). For example: '"C:/Program Files/Circuitscape/cs_run.exe"' ***NOTE: Double quotation used***
Neighbor.Connect	Select 4 or 8 to designate the connection scheme to use in CIRCUITSCAPE (Default = 8)
Constrained.Max	The fixed maximum resistance value to use during the initial constrained grid search (Default = 100)
Initial.shape	The initial shape parameters to test in constrained grid search (Default = c(seq(0.2,1,by=0.2),seq(1.25,10.75,by=0.75)))
Bootstrap	Logical,if TRUE, specify the number of bootstrap iterations for 'boot.iters'
boot.iters	Number of bootstrap iterations (Default = 10,000)
Sample_Proportion	Proportion of samples to be included in each bootstrap iteration (Default = 0.75)

Value

Results in an object with the necessary components to run other the other functions

Examples

# Example.dir <- "C:/Example/"

# 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/4.0/Circuitscape/cs_run.exe"',Neighbor.Connect=8,Results.dir=paste0(Example.dir,"Results/"),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)
  

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