Home

hivclustering documentation

1. hivnetworkcsv: the workhorse of the package which consumes pairwise distance files (and, optionally, other sources of data) and infers the molecular transmission network subject to a variety of user-selectable parameters

2. hivnetworkannotate : imports network node attributes (read from a .csv, .tsv, or .json) to a JSON file output by hivnetworkcsv

3. TNS : assuming sequences have associated sampling dates, computes the transmission network score (TNS), defined by Little et al. Higher TNS is somewhat predictive of whether or not nodes in a network will accrue new edges in the future.