Initial release. Clean reimplementation of the modern geotax workflow
for predicting species interactions from phylogenetic distance:
prepare_pair_data(), fit_phylopred_model(),
compare_phylopred_slopes() — pairwise host-sharing logistic models
and formal slope comparison between clades.bootstrap_phylopred_model(), cluster_bootstrap_phylopred(),
phylopred_confidence_ellipse() — parasite-cluster bootstrap and
joint intercept-slope uncertainty.evaluate_phylopred_model() — McFadden/Tjur pseudo-R2, AUC, and
grouped cross-validated AUC.host_threshold_metric() — presence-only threshold efficiency
f_gamma = a / (gamma * b + c) over the prediction threshold.phylo_partial_roc() — phylogenetic partial ROC (sensitivity vs
fraction of the phylogeny predicted suitable) with bootstrap
ratio against a random-ranking null.fit_phylopred_pu() — positive-unlabeled host prediction with
xplus on phylogenetic features.validate_host_prediction() — leave-hosts-out validation for both
the GLM and PU routes.poulin_std() — Poulin and Mouillot's (2003) average taxonomic/
phylogenetic distinctness index S_TD and its sampling variance, for
any distance matrix (taxonomic steps or phylogenetic distances).taxonomic_step_matrix() — builds the classic 1-5 taxonomic step
matrix from a genus/family/order/class hierarchy table.host_specificity_index() — applies poulin_std() to every
parasite in an interaction table, for contrasting S_TD against
host_threshold_metric()'s model-based host range b*.fish_tree (Fish Tree of Life subtree, CC0),
beetleTreeInteractions, phy_dist.