Calculate isolate-isolate co-location overlap

For every ordered pair of isolates, counts the days on which the two patients were in the same place in trace_mat, within the window from the donor's previous surveillance date up to the recipient's collection date. This is the concurrent (spatiotemporal) overlap; for indirect overlap via a shared location at different times, see isolate_isolate_sequential_overlap().

Usage

isolate_isolate_overlap(isolate_lookup, trace_mat)

Arguments

isolate_lookup

A lookup table for isolates and their cluster assignments with other relevant epidemiological information. See get_isolate_lookup().

trace_mat

A patient-by-date matrix of location occupancy (patients in rows, dates in columns); a positive value marks a patient's location on a given day.

Value

A data frame with columns iso_donor, iso_recipient and overlap_days.