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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.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.