Calculate isolate-isolate sequential overlap

This function calculates the sequential overlap between isolates in a given trace matrix. Sequential overlap counts the number of days where the recipient is at a location that the donor had previously been at (on a strictly earlier day), capturing potential indirect transmission via shared locations.

Usage

isolate_isolate_sequential_overlap(isolate_lookup, trace_mat)

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().

trace_mat

A matrix with rows representing days and columns representing patients.

Value

A data frame with columns: iso_donor, iso_recipient, overlap_days.