wiwMedTree: Median transmission tree

In treespace: Statistical Exploration of Landscapes of Phylogenetic Trees

Median transmission tree

Description

Function to find the median of a list of transmission scenarios

Usage

wiwMedTree(matList, sampled = NULL, weights = NULL)

Arguments

matList	a list of matrices, each of which is the output of findMRCIs$mrciDepths
sampled	a vector of node IDs which corresponds to those nodes which are sampled cases
weights	optional vector of weights to correspond to the entries of matList

Value

Returns three objects:

• centre: the mean of the matList entries, restricted to the sampled cases

• distances: for each entry of matList, its distance from centre

• mindist: the minimum of distances

• median: the number of the median entry of matList, i.e. the one(s) which achieve the mindist from the centre.

Author(s)

Michelle Kendall [e-mail]

Examples

# create some simple "who infected whom" scenarios:
tree1 <- cbind(Infector=1:5,Infectee=2:6) 
tree2 <- cbind(Infector=c(1,5,2,2,3),Infectee=2:6)
tree3 <- cbind(Infector=c(2,2,3,4,5),Infectee=c(1,3,4,5,6)) 
# create list of the MRCI depth matrices:
matList <- lapply(list(tree1,tree2,tree3), function(x) findMRCIs(x)$mrciDepths)

# median tree, assuming all cases are sampled:
wiwMedTree(matList)
# median tree when cases 1, 2 and 4 are sampled:
wiwMedTree(matList, sampled=c(1,2,4))

treespace documentation built on Sept. 8, 2023, 6:04 p.m.