Package index • transclust

Transmission cluster detection algorithms

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

get_tn_clusters_snp_thresh(): Perform clustering of 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.

intra_cluster_genetic_var_analysis(): Analyze Intra-Cluster Genetic Variation
intra_cluster_genetic_distances(): Compute Genetic Distances
compute_cluster_duration_metrics(): Compute Cluster Duration Metrics
cluster_overlap_perm_test(): Permutation test for cluster overlap fractions

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

cluster_contingency_table(): Create Contingency Table from Two Cluster Assignments
adjusted_mutual_information(): Adjusted Mutual Information from Cluster Assignments
ami_from_contingency(): Adjusted Mutual Information from Contingency Table
adjusted_rand_index(): Adjusted Rand Index from Cluster Assignments
ari_from_contingency(): Adjusted Rand Index from Contingency Table
fraction_convert_same_source(): Fraction of Converts with Same Source Across Cluster Assignments
fraction_convert_same_source_from_lookups(): Fraction of Converts with 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 overlap
isolate_isolate_sequential_overlap(): Calculate isolate-isolate sequential overlap
cluster_isolate_overlap(): Calculate isolate-isolate overlap for clusters
fraction_converts_with_overlap(): Calculate the fraction of converts with overlap
categorize_cluster_overlap(): Categorize cluster overlap
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(): Get SNP distance matrix from DNA alignment constructed using a model of DNA evolution.
get_phylo_tree(): Get phylogenetic tree using neighbor-joining or maximum parsimony method.
get_isolate_lookup(): Create a lookup table for isolates along with their cluster assignments.
get_non_single_patient_clusters(): Get non-single patient clusters from a vector of cluster assignments.
remove_singleton_clusters(): Remove singleton clusters from a vector of cluster assignments.