View source: R/infer_multittree_share_param.R
infer_multittree_share_param | 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".
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,
delta_t = 0.01,
verbose = F
)
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) |
delta_t |
Grid precision (smaller is better but slower) |
verbose |
Whether or not to use verbose mode (default is false) |
list the same size as input, each element contains posterior transmission trees inferred from corresponding phylogenetic tree
Yuanwei Xu
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.