Run_CS: Run CIRCUITSCAPE in R

In wpeterman/ResistanceGA: Optimize resistance surfaces using genetic algorithms

Run CIRCUITSCAPE in R

Description

Execute CS from R

Usage

Run_CS(CS.inputs, 
r, 
CurrentMap = FALSE, 
full.mat = FALSE,
EXPORT.dir = NULL, 
output = "matrix", 
hidden = TRUE)

Arguments

CS.inputs	Object created from running CS.prep function
r	Accepts two types of inputs. Provide either the path to the resistance surface file (.asc) or specify an R RasterLayer object
CurrentMap	Logical. If TRUE, the cumulative current resistance map will be generated during the CS run (Default = FALSE)
full.mat	Logical (Default = FALSE). If TRUE, the full distance matrix will be generated as an R object, rather than just the lower half of the distance matrix.
EXPORT.dir	Directory where CS results should be written.Only specify if Circuitscape current map outputs are requested. It is critical that there are NO SPACES in the directory, as this may cause the function to fail.
output	Specifiy either "matrix" or "raster". "matrix" will return the lower half of the pairwise resistance matrix (default), while "raster" will return a raster object of the cumulative current map. The raster map can only be returned if CurrentMap=TRUE
hidden	Logical. If TRUE (Default), then no output from CIRCUITSCAPE will be printed to the console. Only set to FALSE when trying to troubleshoot/debug code.

Value

Vector of CIRCUITSCAPE resistance distances (lower half of "XXX_resistances.out") OR a full square distance matrix if 'full.mat' = TRUE. Alternatively, a raster object of the cumulative current map can be returned when CurrentMap = TRUE and output = "raster".

Author(s)

Bill Peterman <[e-mail]>

Examples

 
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## *** TO BE COMPLETED *** ##

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wpeterman/ResistanceGA documentation built on Nov. 20, 2023, 11:50 p.m.