get_chain: Get transmission chains

In thednainus/HIVepisimAnalysis: Functions to analyse results from network analysis

Get transmission chains

Description

Get transmission chains

Usage

get_chain(df1, tm)

Arguments

df1	Dataframe containing information of summarized results obtained with phyloscanner after running the function summarize_trans.
tm	Transmission matrix containing the information of who transmitted whom.
all_trans	List of dataframes containing the transmission chains for each ID.

Details

This function will go over each transmission to create a "transmission chain from ID1 to ID5, for example. This will help indentify in which circunstances phyloscanner indetified two IDs as a transmission pair, when they were not one.

Value

A dataframe with the transmission chain and the time of transmissions

thednainus/HIVepisimAnalysis documentation built on Sept. 21, 2023, 7:32 a.m.