Package: ResistanceGA2 1.2.0

Overview | Julia Setup | Example Inputs | Pairwise Circuitscape with INI-Style Options | Working from R Objects Instead of Manual Files | Advanced mode with source and ground rasters | Included pairs from an R table | Reclassification tables from R | Existing Paths Still Work | Inspecting the Generated INI | Return Modes | Relationship to the Optimization Workflow | Quick reference: direct Circuitscape control | Summary of key functions | See also

Key Changes from ResistanceGA | Spatial classes: terra only | Removed features | New features in ResistanceGA2 | What Is ResistanceGA2? | Isolation by Distance, Resistance, and Environment | The Conceptual Workflow | Installation | Package Data Overview | Resistance Surfaces | Sample Locations | The raster_orig Dataset | Precomputed Pairwise Outputs | The Four-Step Workflow | Step 1: Prepare Genetic Algorithm Settings with GA.prep() | Step 2: Prepare Distance Engine Inputs | Using gdistance | Using Julia / Circuitscape | Step 3: Run Optimization | Multisurface optimization | All-combinations analysis | Step 4: Interpret and Compare Results | Transformations and Inspection | Visualizing Transformations | Quick reference: first complete workflow | Summary of key functions | Key Terms Glossary | See also | Tips for New Users | References

Overview | Design Choices | Demo Data | Step 1: Build Pairwise Geographic and Environmental Covariates | Step 1a: Check Predictor Overlap Before Fitting Models | Step 2: Fit Baseline MLPE Models Before Optimization | Optional: Multiple Dyadic Random Effects | Step 3: Prepare the Conditional IBR Workflow | Step 4: Run Single-Surface IBR Models Conditional on IBE | Step 5: Run a Multi-Surface IBR Model Conditional on IBE | Step 6: Generate Full Analysis Outputs Outside the Vignette | Step 7: Load and Explore Saved Outputs | Interpretation | Quick reference: conditional IBE and IBR workflow | Summary of key functions | See also

Why Transform Resistance Surfaces? | The Transformation Parameter Space | Shape | Max | The Eight Transformation Families | Monomolecular Families | Monomolecular | Reverse Monomolecular | Inverse Monomolecular | Inverse-Reverse Monomolecular | Ricker Families | Ricker | Reverse Ricker | Inverse Ricker | Inverse-Reverse Ricker | Comparing All Eight Families | The Flat Distance Transformation | Choosing Transformation Families | Practical Guidance | The select.trans Argument | Applying Transformations Directly | Resistance.tran() | Plot.trans() | How the GA Searches Transformation Space | Collapsing to the Distance Solution | Overfitting Concerns | Summary of Transformation Families | Quick reference: choosing and applying transformations | Summary of key functions | See also | References

Background | Resistance Modeling in Landscape Genetics | The Genetic Algorithm Approach | The MLPE Framework | Thoughts on Optimization | Choosing an Objective Function | Counting Parameters: k.value | Transformation Families | Example Data and Preparation | The Dataset | Preparing GA Settings | Preparing gdistance Inputs | Single-Surface Optimization | Running SS_optim | Multi-Surface Optimization | Loading and Displaying Results | Recovered Transformation Parameters | Interpreting SS_optim Output | Running MS_optim | Loading Multi-Surface Results | Percent Contribution | Reconstructing the Composite Surface | All-Combinations Analysis | When to Use all_comb | Setting Up all_comb | Loading all_comb Results | Bootstrap Analysis | Why Bootstrap? | Running Resist.boot | Loading Bootstrap Results | Interpreting Bootstrap Results | Comparing Single-Surface, Multi-Surface, and Null Models | Diagnostic Plots | Quick reference: full optimization workflow | Summary of key functions | See also | Tips for Running Full Analyses | References

Overview | Step 1: Install Julia | Downloading Julia | Verifying the Julia Installation | Step 2: Install Circuitscape.jl | Installing JuliaConnectoR | Step 3: Configure R to Find Julia | How ResistanceGA2 Manages Julia Paths | Finding Julia's Path Automatically | Step 4: Verify the Connection | Step 5: Prepare a Small Julia Example | Set Up Sample Data | Create Julia Inputs with jl.prep() | jl.prep() Parameter Details | Computing Pairwise Resistance Distances | Run_CS.jl() for Pairwise Distances | Run_CS.jl() Parameter Details | Direct Circuitscape runs with .ini-style control | Current maps | Computing Current Maps | Julia in Optimization Workflows | Tuning and Troubleshooting | Comparing gdistance and Julia Outputs | Conceptual Similarity | Comparing Outputs | Performance Considerations | Landscape Size | Number of Populations | Environment Management for Julia Packages | Checking Your Julia Environment | Multiple Julia Versions | Updating Circuitscape.jl | Troubleshooting | Julia Not Found | Circuitscape Not Found | Slow Startup | Out of Memory | File Permission Errors on Windows | Connection Drops Mid-Optimization | Summary | Quick reference: the Julia workflow in one block | Summary of key functions | See also | References