align_phylopred_inputs
                        Align incidence matrix and phylogenetic
                        distance matrix
beetleTreeInteractions
                        Beetle tree interaction table.
bootstrap_phylopred_model
                        Bootstrap a phylopred logistic regression model
cluster_bootstrap_phylopred
                        Cluster bootstrap for pairwise host-sharing
                        models
compare_phylopred_slopes
                        Compare host-sharing slopes between two clades
evaluate_phylopred_model
                        Evaluate the predictive capacity of a pairwise
                        host-sharing model
extract_phylopred_coefficients
                        Extract coefficients from a phylopred model or
                        bootstrap object
fish_tree               Phylogenetic tree of marine fish hosts of
                        Caligus and Lepeophtheirus
fit_phylopred_model     Fit a phylopred logistic regression model
fit_phylopred_pu        Positive-unlabeled host prediction via xplus
                        (PLUS algorithm)
host_specificity_index
                        Host specificity index (S_TD) for every
                        parasite in an interaction table
host_threshold_metric   Threshold metric f_gamma for predicted host
                        suitability
phy_dist                Phylogenetic distance matrix among host data on
                        phylopred
phylo_partial_roc       Phylogenetic partial ROC (Peterson, Papes &
                        Soberon 2008 analogue)
phylopred_confidence_ellipse
                        Joint confidence ellipse for intercept and
                        slope
poulin_std              Poulin and Mouillot taxonomic/phylogenetic
                        distinctness index (S_TD)
predict_phylopred_probability
                        Predict host susceptibility probabilities from
                        logistic regression coefficients
prepare_incidence_matrix
                        Prepare an incidence matrix from an interaction
                        table
prepare_pair_data       Build a pairwise host-sharing data set from an
                        interaction table
taxonomic_step_matrix   Build a taxonomic step-distance matrix (Poulin
                        & Mouillot scale)
validate_host_prediction
                        Leave-hosts-out validation of host predictions
