SimulatedOutbreakGenealogy: Simulated outbreaks with genealogies

Description

A few functions to simulate a rather simple outbreak where the infectiousness is not homogeneous, and then to extract a genealogy for the simulated infections. The outbreak simulation uses the simNHP.fun function in the NHPoisson package. Functions makephylotree and sortmyepi are intended for use by getgenealogy, not direct use.

Usage

maketranstree(lambda,duration=1,NumCases=50)
	getgenealogy(epirecord,epsilon=0.01)

Arguments

lambda

A vector specifying the rate of the non-homogeneous Poisson process over time (ie the infectivity). The size of lambda also specifies the resolution with which the infection process is simulated.

duration

The duration of infectiousness (fixed).

NumCases

An integer specifying the desired number of cases in the outbreak.

epirecord

A simulated outbreak returned by maketranstree

epsilon

A small number to ensure that getgenealogy returns positive branch lengths. This is relevant when individuals recover/are sampled in the same time step in which they became infected or when individuals infect several others in the same time step.

Value

maketranstreeA matrix with 4 named columns: Infectee, Infector, InfnTime, RecTime corresponding to the case number of the infected individual, the individual infecting them, the time of infection, and the individual's recovery time (same as the sampling time).
getgenealogyAn object of class phylo4 in which tips correspond to cases in the simulated outbreak and internal nodes correspond to the infection events among them.

Details

maketranstree generates a transmission tree, starting with one infectious individual, where the infectiousness through time is given by the argument lambda. getgenealogy extracts a genealogy from the simulated transmission tree returned by maketranstree. It assumes that branching points in the genealogy correspond to infection events in the outbreak and that cases are sampled at the time of recovery.

Examples

Run this code

# specify an inhomogeneous rate of new infections
lambda<- c(rep(0.2,10), rep(0.1,10)) # twice as infectious in the first half of the 
# infectious period, with a mean number of 3 secondary cases

## Create a simulated outbreak
 epirecord<-maketranstree(lambda,duration=2,NumCases=30)

## Extract the genealogy as a phylo4 object
simgeneal<-getgenealogy(epirecord)

# Intermediate functions: 
  # creates the phylo4 object from a list of edges and lengths. 
	# makephylotree(Edges,Lengths,Root) 
	
	sortmyepi(epirecord) # sorts the rows of the simulated epidemic