Feature/relationship matrix#95
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Introduces an optional `relationship` argument to `calculate_adjacency_score()` and `speed()`, letting neighbour pairs contribute a graded similarity from a user-supplied matrix instead of a strict identity match. `speed()` validates and pre-flattens the matrix once before the SA loop via the new exported `prep_relationship()` helper. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Walks through a 16-treatment, 4-group blocked design and contrasts the default identity-only optimisation against `speed()` driven by a relationship matrix. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
.Rbuildignore: exclude .claude/ and Rplots.pdf from package builds. .gitignore: exclude *.local.json. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
speed() forwards these explicitly from optim_params() while also splatting `...` to the objective function, so a direct `speed(..., bal_weight = 2)` triggered "matched by multiple actual arguments". `speed()` now stops with a message pointing the caller at `optimise_params = optim_params(...)`. Factor the dots guard and the pre-loop relationship prep into `.reject_optim_params_in_dots()` and `.prep_dots()` helpers. Vignette `genetic_relationship.qmd` gains a "Per-Pair Similarities" example with closely-related-pair highlighting. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…eature/relationship-matrix
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The rendered vignette: genetic_relationship.html