transroutes: Assessment of transmission routes using theoretical SNP...
In seedy: Simulation of Evolutionary and Epidemiological Dynamics

Description Usage Arguments Details Value See Also Examples

Calculates likelihood and posterior probability of each potential transmission route using a geometric-Poisson approximation of SNP distance.

1 2	transroutes(ID, GD, sample.times, inf.times, rec.times=NULL, mut.rate, eq.size, bottle.size=1, p.level=0.95, geninterval=NULL, summary=TRUE)

`ID`	Vector of individual IDs.
`GD`	Matrix of genetic distances, with the [i,j]-th entry corresponding to the genetic distance between samples from the ith and jth entry of `ID`.
`sample.times`	Vector of genome sampling times (same length as `ID`).
`inf.times`	Vector of infection times (same length as `ID`).
`rec.times`	Vector of recovery times (same length as `ID` if specified).
`mut.rate`	Mutation rate.
`eq.size`	Equilibrium within-host effective population size.
`bottle.size`	Size of population bottleneck.
`p.level`	Probability level at which to reject potential transmission routes.
`geninterval`	Generation interval (if `bottle.size`>1).
`summary`	Should a summary for each ID be printed to screen?

Calculates the likelihood and posterior probability (given a flat prior) for each potential transmission route, as well as indicating which transmission routes would be rejected at a given probability level. If recovery times are not specified, each individual is assumed to be infectious for the duration of the outbreak.

Returns calculated values:

`maxpostsource`	Vector of maximum posterior probability transmission sources corresponding to `ID`.
`likelihood`	A matrix of likelihood values from the geometric-Poisson distribution. The [i,j]th entry provides the likelihood that the i-th individual infected the j-th individual.
`posterior`	A matrix of posterior transmission probabilities. The [i,j]th entry provides the posterior probability that the i-th individual infected the j-th individual.
`closestsource`	A list of the individuals carrying the most genetically similar genotype. Each entry corresponds to `ID`.
`reject`	Matrix indicating whether a transmission route would be rejected at the specified probability level. The [i,j]th entry is equal to 1 if the route from i to j is rejected at this level.

expsnps

  data(transmission)
  W <- transmission
  ID <- unique(W$sampledata[,1])
  GD <- gd(W$sampledata[,3], W$libr, W$nuc, W$librstrains)
  
  sample.times <- W$sampledata[,2]
  inf.times <- numeric(length(ID))
  rec.times <- numeric(length(ID))
  truesource <- numeric(length(ID))
  for (i in 1:length(ID)) {
    inf.times[i] <- W$epidata[which(W$epidata[,1]==ID[i]),2]
    rec.times[i] <- W$epidata[which(W$epidata[,1]==ID[i]),3]
    truesource[i] <- W$epidata[which(W$epidata[,1]==ID[i]),4]
  }
  
  K <- transroutes(ID=ID, GD=GD, sample.times=sample.times, inf.times=inf.times, 
                   rec.times=rec.times, mut.rate=0.01, eq.size=5000, 
                   bottle.size=1, p.level=0.95, summary=TRUE)
  truesource
  K$maxpostsource