findMRCIs: Find MRCIs

In thibautjombart/treescape: Statistical Exploration of Landscapes of Phylogenetic Trees

Description

Function to find the most recent common infector (MRCI) matrix from "who infected whom" information.

Usage

findMRCIs(wiw)

Arguments

wiw	a two-column matrix where the first column represents the infectors and the infectees; each row corresponds to a transmission event from an infector to an infectee.

Value

Returns three objects:

• sourceCase: the number of the node which is the source case, i.e. the common infector of all cases (outputs a warning if there is more than one source case).

• mrcis: a matrix where, for each pair of individuals i and j, the entry (i,j) is the node number of their MRCI. Note that if i infected j then this entry is i itself.

• mrciDepths: a matrix where, for each pair of individuals i and j, the entry (i,j) is the depth of their MRCI, defined as the number of edges from the source case. The source case has depth zero, its direct infectees have depth 1, and so on.

Author(s)

Michelle Kendall [e-mail]

Examples

## a simple who infected whom matrix:
tree1 <- cbind(Infector=1:5,Infectee=2:6) 
findMRCIs(tree1)

thibautjombart/treescape documentation built on May 31, 2019, 10:38 a.m.