SS_optim: Single surface optimization

In wpeterman/ResistanceGA: Optimize resistance surfaces using genetic algorithms

Single surface optimization

Description

Optimize all surfaces contained in a directory using a genetic algorithm executed with the ga function in the Genetic Algorithms package GA

Usage

SS_optim(CS.inputs, 
 gdist.inputs, 
 jl.inputs,
 GA.inputs,
 dist_mod, 
 null_mod,
 diagnostic_plots = TRUE)

Arguments

CS.inputs	Object created from running CS.prep function. Defined if optimizing using CIRCUITSCAPE
gdist.inputs	Object created from running gdist.prep function. Defined if optimizing using gdistance
jl.inputs	Object created from running jl.prep function. Defined if optimizing using CIRCUITSCAPE run in Julia
GA.inputs	Object created from running GA.prep function
dist_mod	Logical, if TRUE, a Distance model will be calculated and added to the output table (default = TRUE)
null_mod	Logical, if TRUE, an intercept-only model will be calculated and added to the output table (default = TRUE)
diagnostic_plots	Plotting and saving of diagnostic plots (Default = TRUE)

Value

This function optimizes resistance surfaces in isolation. Following optimization of all surfaces, several summary objects are created.

1. Diagnostic plots of model fit are output to the "Results/Plots" directory that is automatically generated within the folder containing the optimized ASCII files.

2. A .csv file with the Maximum Likelihood Population Effects mixed effects model coefficient estimates (MLPE_coeff_Table.csv)

3. Three summary .csv files are generated: CategoricalResults.csv, ContinuousResults.csv, & All_Results_AICc.csv. These tables contain AICc values and optimization summaries for each surface.

All results tables are also summarized in a named list ($ContinuousResults, $CategoricalResults, $AICc, $MLPE, $MLPE.list, $cd, $k)
The lmer model objects stored $MLPE.list are fit using Restricted Maximum Likelihood
$cd is a list of the optimized cost pairwise distance matrices and $k is a table of the surface names and number of parameters used to calculate AICc. These two objects can be passed to Resist.boot to conduct a bootstrap analysis.

Author(s)

Bill Peterman <[e-mail]>

Examples

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