infer_multiTTree_shareParam: Simultaneously infer transmission trees given phylogenetic...
In JamesStimson/transnp: Transmission inference using SNP data

Description Usage Arguments Value Author(s)

Simultaneously infer transmission trees given phylogenetic trees constructed from clusters of sequences. User can specify any parameter(s) to be shared by providing a character vector of parameter names to the argument "share".

infer_multiTTree_shareParam(ptree_lst, 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 = TRUE, updateOff.r = TRUE,
  updateOff.p = FALSE, updatePi = TRUE, share = NULL,
  startCTree_lst = rep(NA, length(ptree_lst)), updateTTree = TRUE,
  optiStart = TRUE, dateT = Inf)

`ptree_lst`	List of 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
`share`	Character vector of parameters to be shared. For example, share = c("off.r", "off.p") would share the offspring distribution. Allowed parameter names are "neg", "off.r", "off.p" and "pi".
`startCTree_lst`	Optional combined list of trees 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)