Calculate isolate-isolate sequential overlap

For every ordered pair of isolates, counts the days on which the recipient was at a location the donor had occupied on a strictly earlier day, capturing potential indirect transmission via a shared location. Pairs with any concurrent co-location are excluded, since that is direct overlap and is handled by isolate_isolate_overlap().

Usage

isolate_isolate_sequential_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.