Summarize isolate overlap within each cluster — cluster_isolate

For each isolate in a cluster (treated as a recipient), reports whether any other isolate in the same cluster (as a donor) overlaps with it, using the isolate-pair overlaps from isolate_isolate_overlap() or isolate_isolate_sequential_overlap(). Admission-positive isolates are reported as NA, since they were not acquired in the facility.

Only multi-patient clusters are reported by default; set include_singleton_acq to also account for acquisitions sitting in single-patient clusters.

Usage

cluster_isolate_overlap(
  isolate_lookup,
  iso_overlap_df,
  include_singleton_acq = FALSE
)

Arguments

isolate_lookup: A lookup table for isolates and their cluster assignments with other relevant epidemiological information. See get_isolate_lookup().
iso_overlap_df: A data frame of isolate-pair overlaps, from isolate_isolate_overlap().
include_singleton_acq: Whether to evaluate all acquisitions, including those not classified to be a part of multi-patient clusters.

Value

A data frame with columns cluster, isolate_id and overlap.