phylopred 0.1.0

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*.
• Data: fish_tree (Fish Tree of Life subtree, CC0), beetleTreeInteractions, phy_dist.