New module for computing the fraction of nonunique monoclonal infections

[a-hubbard]

Create a new bespoke code module to calculate the fraction of monoclonal infections in a population that are not unique. In other words, the fraction of infections with a COI of 1 that are not clones of one or more other infections in the population. This module is for the transmission intensity workflow. It should take an allele table as an input and output a table with one row and two columns: frac_nonunique and sample_total. sample_total should contain the number of monoclonal infections in that population.