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 |

`sample.times` |
Vector of genome sampling times (same length as |

`inf.times` |
Vector of infection times (same length as |

`rec.times` |
Vector of recovery times (same length as |

`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 |

`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 |

`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 |

`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. |

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ```
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
``` |

seedy documentation built on May 29, 2017, 10:58 a.m.

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