Package index • phylopred

All functions

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