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.