Predicting Species Interactions from Phylogenetic Distance

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Documentation for package ‘phylopred’ version 0.1.0

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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
phylopred_confidence_ellipse Joint confidence ellipse for intercept and slope
phylo_partial_roc Phylogenetic partial ROC (Peterson, Papes & Soberon 2008 analogue)
phy_dist Phylogenetic distance matrix among host data on phylopred
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