Description Usage Arguments Value Author(s) Examples
This function will generate mixed effect model diagnostic plots following optimization with 'Resistance.Optimization'
1 | Diagnostic.Plots(resist.matrix.path, genetic.dist.vec, XLAB, YLAB, plot.dir)
|
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$Results.dir,"Plots/"))" to output PDF in same directory as other response plots) |
This function will produce a single PDF called DiagnotisticPlots containing four plots. 1) The relationship between the optimized resistance value and your pairwise distance provided as a response (genetic distance) 2) Scatter plot of the mixed effect model residuals in relation to resistance distance 3) Distribution of residuals 4) Q-Q plot
Bill Peterman
1 | # Diagnostic.Plots(resist.matrix.path=paste0(Optim.input$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/"))
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.