infer_multittree_share_param {TransPhylo} | R Documentation |
Simultaneously infer transmission trees given phylogenetic trees User can specify any subset of parameters that will be shared by providing a character vector of parameter names to the argument "share".
Description
Simultaneously infer transmission trees given phylogenetic trees User can specify any subset of parameters that will be shared by providing a character vector of parameter names to the argument "share".
Usage
infer_multittree_share_param(
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,
prior_pi_a = 1,
prior_pi_b = 1,
updateNeg = TRUE,
updateOff.r = TRUE,
updateOff.p = FALSE,
updatePi = TRUE,
share = NULL,
startCTree_lst = rep(NA, length(ptree_lst)),
updateTTree = TRUE,
optiStart = 2,
dateT = Inf,
verbose = F
)
Arguments
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 |
prior_pi_a |
First shape parameter of Beta prior for pi |
prior_pi_b |
Second shape parameter of Beta prior for 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 |
Type of optimisation to apply to MCMC start point (0=none, 1=slow, 2=fast) |
dateT |
Date when process stops (this can be Inf for fully simulated outbreaks) |
verbose |
Whether or not to use verbose mode (default is false) |
Value
list the same size as input, each element contains posterior transmission trees inferred from corresponding phylogenetic tree
Author(s)
Yuanwei Xu