Diagnostic.Plots: Create diagnostic plots

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

Description

This function will generate mixed effect model diagnostic plots following optimization with 'Resistance.Optimization'

Usage

Diagnostic.Plots(resist.matrix.path, genetic.dist.vec, XLAB, YLAB, plot.dir)

Arguments

resist.matrix.path	Provide the full path to the square distance matrix produced by Circuitscape (file ending with "_resistances.out") Example: paste0(Optim.input$Results.dir,"Final_CS_Surfaces/XXX_resistances.out"
genetic.dist.vec	Vector of pairwise genetic distances (can supply as "Optim.input$Response.vec" after executing Optim.prep function)
XLAB	Label for x-axis (Defaults to "Estimated resistance")
YLAB	Label for y-axis (Defaults to "Genetic distance")
plot.dir	Directory to output PDF of diagnostic plots (can use "paste0(Optim.input$Results.dir,"Plots/"))" to output PDF in same directory as other response plots)

Value

This function will produce a single PDF called DiagnotisticPlots containing four plots. 1) The relationship between the optimized resistance value and your pairwise distance provided as a response (genetic distance) 2) Scatter plot of the mixed effect model residuals in relation to resistance distance 3) Distribution of residuals 4) Q-Q plot

Author(s)

Bill Peterman

Examples

# Diagnostic.Plots(resist.matrix.path=paste0(Optim.input$Results.dir,"Final_CS_Surfaces/resist1_resistances.out"),genetic.dist.vec=Optim.input$Response.vec,XLAB="Transformed resistance",YLAB="Pairwise distance",plot.dir=paste0(Optim.input$Results.dir,"Plots/"))

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