phyloTop (version 2.1.2)

getLabGenealogy: Create genealogy

Description

Create a labelled genealogy from an epidemiological record

Usage

getLabGenealogy(epirecord, epsilon = 0.001234)

Value

An object of class phylo representing the transmission tree from infectors to infectees.

Arguments

epirecord

an epidemiological record, as output from the function makeEpiRecord. It must be a matrix of at least two rows and with five columns named "Infectee", "Infector", "InfnTime", "RecTime", "DoneFlag".

epsilon

an optional small number to be used for branch lengths which would otherwise be zero.

Author

Caroline Colijn

Michelle Kendall

See Also

makeEpiRecord

Examples

## Generate an epidemiological record:
myepirecord <- makeEpiRecord(c(1,2,3,4))
## make the corresponding genealogy from this record:
mygenealogy <- getLabGenealogy(myepirecord)
plot(mygenealogy)