find_loops_to_fix: Internal function for finding loops to fix

In mrajeev08/treerabid: Reconstruct Rabies Transmission Trees

Internal function for finding loops to fix

Description

Internal function for finding loops to fix

Usage

find_loops_to_fix(links_consensus, case_dates, known_progens, max_cycles = 100)

Arguments

links_consensus	consensus links build within build_consensus_links function
case_dates	data.table with two columns id_case (id of case) and symptoms_started (date symptoms started of case without uncertainty)
known_progens	a numeric vector of case ids for which progenitors are known
max_cycles	how many cycles to look for (if lots of date uncertainty you may want to increase this but it will likely slow things down a lot!)

Value

a numeric vector of case ids for which links should be reassigned

mrajeev08/treerabid documentation built on Oct. 15, 2024, 12:14 p.m.