Calculates the temporal distance between every pair of individuals in an
outbreak based on their Most Recent Common Infector (MRCI).
Usage
find_all_pairwise_distances(outbreak, return_matrix = TRUE)
Arguments
- outbreak
A data frame with 'infectee', 'infector', 'infection_time', and 'removal_time'.
- return_matrix
Logical. If TRUE (default), returns a symmetric $nxn$
numeric matrix. If FALSE, returns a long-format data frame.
Value
If return_matrix is TRUE, a symmetric matrix.
Otherwise, a data.frame containing columns for both IDs, the shared
infector, the infector's infection time, and the calculated distance.
