Calculate isolate-isolate overlap for clusters — cluster_isolate

This function considers every isolate in a cluster as a recipient, and returns if there is any overlap when other isolates in the cluster are the donors.

Usage

cluster_isolate_overlap(isolate_lookup, iso_overlap_df)

Arguments

isolate_lookup: A lookup table for isolates and their clusters assignments which has other relevant epidemiological information. For more information, see get_isolate_lookup().
iso_overlap_df: A data frame with overlap information for isolate pairs. For more information, see isolate_isolate_overlap().

Value

A data frame with columns: cluster, isolate_id, overlap.