Package index • agdist

All functions

calculate_distance(): Calculate pairwise distances between sequences using various methods

dist_pepi(): Compute Pairwise p-Epitope Distance Matrix

dist_string(): Compute Pairwise Normalized String Distances Between Aligned Sequences

dist_substitution(): Pairwise Substitution Distances Between Amino Acid Sequences

dist_temporal(): Compute Temporal Distance Matrix Between Sequences

extract_string_chars(): Extract Specific Characters from a String by Position

extract_year(): Extract 4-digit Years from Strings

generate_FLU_matrix(): Generate FLU Amino Acid Substitution Matrix

generate_grantham_matrix(): Generate Grantham Distance Matrix

get_pepitope_sites(): Retrieve Epitope Residue Sites for Influenza HA Subtypes

pepitope(): Compute p-Epitope Distance Between Two Sequences

racmaps_map_to_distances(): Convert Racmacs Map to Pairwise Distance Matrix

remove_ambiguous_residues(): Remove ambiguous residues from aligned sequences

substitution(): Calculate Substitution Distance Between Amino Acid Sequences

tidy_dist_mat(): Convert a distance matrix to tidy format

tree_to_distances(<default>): Default method for `tree_to_distances`

tree_to_distances(<phylo>): Extract distances from a phylo object

tree_to_distances(<pml>): Extract distances from a pml object

tree_to_distances(): Extract distances from a phylogenetic tree

validate_sequence_input_form(): Validate a sequence vector