Description Usage Arguments Value
Infer transmission tree given a phylogenetic tree
1 2 3 4 5 | inferTTree(ptree, w.shape = 2, w.scale = 1, ws.shape = w.shape,
ws.scale = w.scale, mcmcIterations = 1000, thinning = 1,
startNeg = 100/365, startOff.r = 1, startOff.p = 0.5, startPi = 0.5,
updateNeg = T, updateOff.r = T, updateOff.p = F, updatePi = T,
startCTree = NA, updateTTree = TRUE, optiStart = T, dateT = Inf)
|
ptree |
Phylogenetic tree |
w.shape |
Shape parameter of the Gamma probability density function representing the generation time |
w.scale |
Scale parameter of the Gamma probability density function representing the generation time |
ws.shape |
Shape parameter of the Gamma probability density function representing the sampling time |
ws.scale |
Scale parameter of the Gamma probability density function representing the sampling time |
mcmcIterations |
Number of MCMC iterations to run the algorithm for |
thinning |
MCMC thinning interval between two sampled iterations |
startNeg |
Starting value of within-host coalescent parameter Ne*g |
startOff.r |
Starting value of parameter off.r |
startOff.p |
Starting value of parameter off.p |
startPi |
Starting value of sampling proportion pi |
updateNeg |
Whether of not to update the parameter Ne*g |
updateOff.r |
Whether or not to update the parameter off.r |
updateOff.p |
Whether or not to update the parameter off.p |
updatePi |
Whether or not to update the parameter pi |
startCTree |
Optional combined tree to start from |
updateTTree |
Whether or not to update the transmission tree |
optiStart |
Whether or not to optimise the MCMC start point |
dateT |
Date when process stops (this can be Inf for fully simulated outbreaks) |
posterior sample set of transmission trees
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