Package index • hospitraceR

Transmission cluster detection algorithms

A collection of algorithms for detecting transmission clusters in epidemiological data.

get_tn_clusters_snp_thresh(): Cluster isolates using a hard SNP distance cutoff
get_tn_clusters_sv_index(): Identify transmission clusters based on the number of shared variants

Functions for statistical analysis of transmission clustering results.

cluster_pairwise_distances(): Compute intra-cluster SNP-distance summaries
cluster_inter_distances(): Compute per-cluster nearest-neighbor SNP distances
compute_genetic_distances_by_cluster(): Compute genetic distances by cluster
intra_cluster_duration_metrics(): Compute intra-cluster duration metrics
compute_duration_metrics_by_cluster(): Compute duration metrics by cluster

Functions for comparing different cluster assignments using contingency tables, information-theoretic measures, and source concordance.

cluster_contingency_table(): Create a contingency table from two cluster assignments
adjusted_mutual_information(): Compute the adjusted mutual information from cluster assignments
ami_from_contingency(): Compute the adjusted mutual information from a contingency table
adjusted_rand_index(): Compute the adjusted Rand index from cluster assignments
ari_from_contingency(): Compute the adjusted Rand index from a contingency table
fraction_convert_same_source(): Compute the fraction of converts with the same source across cluster assignments
fraction_convert_same_source_from_lookups(): Compute the fraction of converts with the same source from isolate lookups

Functions for analyzing patient overlap within and between transmission clusters, and categorizing clusters by epidemiological patterns.

isolate_isolate_overlap(): Calculate isolate-isolate co-location overlap
isolate_isolate_sequential_overlap(): Calculate isolate-isolate sequential overlap
cluster_isolate_overlap(): Summarize isolate overlap within each cluster
fraction_convert_events_with_overlap(): Calculate the fraction of convert events with overlap
categorize_cluster_overlap(): Categorize cluster overlap
flatten_cluster_overlap_categorization(): Flatten cluster-overlap categorization to a data frame
cluster_overlap_perm_test(): Permutation test for cluster overlap fractions
cluster_patient_categorization(): Categorize patients within clusters by epidemiological status
flatten_cluster_patient_categorization(): Flatten cluster-patient categorization to a data frame

A collection of utility functions for this package.

get_snp_dist_matrix(): Compute a pairwise SNP distance matrix from a DNA alignment
get_phylo_tree(): Build a phylogenetic tree by neighbor-joining or maximum parsimony
get_isolate_lookup(): Create a lookup table for isolates along with their cluster assignments
get_non_single_patient_clusters(): Get clusters containing more than one patient
remove_singleton_clusters(): Remove singleton clusters from a vector of cluster assignments