NEWS

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ResistanceGA2 1.2.0

• Expanded documentation for all exported functions, fitted-result classes, model outputs, and interpretation
• Revised all six vignettes to use the current API and provide clearer workflow guidance and result interpretation
• Added informative print, summary, and response-plot methods for single-surface and multisurface optimization results
• Reworked Diagnostic.Plots() to support vector, matrix, dist, and file inputs and to return the fitted model and plotted data
• Corrected Resist.boot() to calculate holdout RMSE and added reproducible Windows-compatible parallel bootstrap execution
• Added explicit bootstrap parallel controls to all_comb() and protected existing result directories from silent deletion
• Hardened Windows parallel optimization by safely transferring SpatRaster inputs to workers and added regression coverage for single-surface, multisurface, and bootstrap workflows
• Improved Julia discovery, environment restoration, Circuitscape loading, and current-map handling with live Julia integration tests
• Reconciled optional dependencies and namespace imports for package-check compliance
• Added CRAN submission metadata and losslessly compressed bundled fitted-result objects to reduce package size
• Updated fixed-effect formula extraction for compatibility with current lme4 and reformulas releases

ResistanceGA2 1.1.23

• Corrected the Beninde et al. 2024 reference title in the ResistanceGA and Surface_Transformations vignettes
• Replaced an incorrect Row et al. 2010 reference entry with the correct citation in the ResistanceGA vignette
• Removed a misattributed Beninde et al. 2024 citation from the R-squared objective-function guidance in the ResistanceGA vignette
• Verified all remaining vignette and documentation references against published sources

ResistanceGA2 1.1.22

• Added a package hex logo (man/figures/logo.png), displayed in the README and on the package help page

ResistanceGA2 1.1.21

• Corrected the GettingStarted vignette argument table defaults for run (25), parallel (FALSE), and pop.size (auto-computed)
• Fixed the README description of rga2_demo_covariates to list all six raster layers (cti, err27, ffp, gsp, hli, nlcd)
• Corrected the Beninde et al. 2024 reference title in the GettingStarted vignette
• Added a Julia and JuliaConnectoR version-compatibility note to the Julia_Guide vignette, including a Windows Store alias caveat

ResistanceGA2 1.1.19

• Routed jl.prep kept-pair outputs more directly through the shared MLPE pair-metadata workflow while preserving legacy return objects
• Added benchmark-based recommend_commute_settings() guidance for choosing exact versus aggregate commute-distance settings
• Added focused regression coverage for jl.prep pop2ind/pairs_to_include alignment and commute recommendation thresholds
• Updated README and workflow vignettes to demonstrate recommend_commute_settings() for choosing commute-distance optimization settings
• Added graph_to_keep() to convert population graphs, adjacency matrices, or edge lists into pair-pruning vectors for gdist.prep() and jl.prep()
• Documented graph-based pair pruning in the gdistance and Julia prep helpers
• Added min.max_dist support in gdist.prep() using the selected-pair keep-vector workflow
• Expanded jl.prep() population-level covariates for pop2ind workflows before applying selected-pair filters
• Added a local-only future_dev_ideas.md planning note to .gitignore so future methodological ideas can be kept in the repo workspace without being tracked

ResistanceGA2 1.1.18

• Refactored jl.prep to build Julia MLPE workflow data, random-effect terms, and kept-pair subsets through the shared pair-metadata path while preserving legacy return values
• Added focused regression coverage for jl.prep pairs_to_include, pop2ind, and nb combinations

ResistanceGA2 1.1.17

• Routed all MLPE.lmm_coef coefficient-extraction branches through the dyad-aware MLPE backend while preserving legacy file-output workflows
• Added focused regression coverage for file-based MLPE coefficient extraction metadata reuse and formula-driven predictor refresh

ResistanceGA2 1.1.16

• Stabilized the categorical optimizer regression test against platform-specific non-finite likelihoods from near-perfect fixture data

ResistanceGA2 1.1.15

• Pre-aggregated resistance stacks for opt-in aggregate gdistance commute-distance GA fitness evaluation while keeping final reported gdistance distances exact
• Added focused helper-level tests for approximate gdistance optimization setup without running full GA searches

ResistanceGA2 1.1.14

• Optimized gdistance commute runs with batched sparse solves and selected-pair gdistance runs by reusing endpoint distance calculations
• Added a vectorized sparse transition builder for the default gdistance transition function on projected 4- and 8-neighbor rasters
• Added a vectorized projected-raster geographic correction path for gdistance transition matrices
• Tuned the sparse Cholesky strategy used by fast gdistance commute-distance solves on large rasters
• Reduced peak memory and solve time for exact gdistance commute-distance runs by solving endpoint right-hand sides in blocks
• Cached projected-raster gdistance transition geometry across repeated calls with identical raster geometry and directions
• Added an opt-in aggregate approximation for iterative gdistance commute-distance optimization runs
• Added benchmark scripts comparing optimized gdistance commute runs with Julia/Circuitscape and aggregate approximations

ResistanceGA2 1.1.13

• Made the Julia_Guide connection-verification chunks display-only so vignette rebuilds do not depend on starting Julia during package checks

ResistanceGA2 1.1.12

• Made the Julia_Guide vignette detect Julia automatically so vignette rebuilds do not fail on systems without a local Julia installation
• Restored normal vignette builds in the GitHub Actions package-check workflow

ResistanceGA2 1.1.11

• Excluded GitHub workflow files from built package contents and aligned CI package checks with the standard no-vignette pre-check workflow

ResistanceGA2 1.1.10

• Updated the GitHub Actions package-check workflow to skip vignette builds on CI runners

ResistanceGA2 1.1.9

• Updated package examples and vignettes to use packed-raster-safe resistance surface handling
• Fixed jl.prep's internal Julia test raster export to work with the current bundled surfaces
• Added a GitHub Actions workflow that runs package checks on substantive pushes and pull requests

ResistanceGA2 1.1.8

• Routed bootstrap, diagnostic, and legacy coefficient MLPE fits through the dyad-aware fitting backend
• Preserved legacy MLPE.lmm numerical behavior while aligning workflow pair metadata with the new MLPE machinery

ResistanceGA2 1.1.7

• Clarified that mlpe and mlpe_data are the preferred standalone MLPE API
• Marked mlpe_rga, MLPE.lmm, and To.From.ID as legacy compatibility helpers in documentation

ResistanceGA2 1.1.6

• Fixed recursive printing of bootstrap tables in all_comb and bootstrap summaries

ResistanceGA2 1.1.5

• Fixed all_comb bootstrap metadata alignment when Null models are included

ResistanceGA2 1.1.4

• Integrated the dyad-aware MLPE interface and pairwise environmental helper workflow into main
• Updated IBE/IBR and Julia vignettes for the new MLPE formulation and packed terra demo objects
• Fixed Plot.trans duplicate plotting, Run_gdistance example behavior, and in-memory current-map returns

ResistanceGA2 1.1.2

• Fixed Windows parallel optimization for raster-based workflows
• Added IBE/IBR vignette builder support for multi-core execution

ResistanceGA2 1.1.1

• Expanded unit tests
• Improved error catching

ResistanceGA2 1.1.0

• Working package with unit tests

ResistanceGA2 1.0.1

• Vignette update

ResistanceGA2 1.0.0

• Initial commit of the updated package