sample.partial.tt: Resample the subtree rooted at any tree node, keeping the...

In STraTUS: Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny

Description

Resample the subtree rooted at any tree node, keeping the annotations for the rest of the tree fixed

Usage

sample.partial.tt(
  generator,
  count = 1,
  unsampled = 0,
  starting.node = phangorn::getRoot(generator$tree),
  existing = NULL,
  check.integrity = TRUE,
  draw = count == 1,
  igraph = FALSE,
  verbose = FALSE
)

Arguments

generator	A list of class tt.generator produced by tt.generator.
count	How many transmission trees to sample.
unsampled	The number of unsampled hosts in the transmission chain. (The whole transmission chain, even if only part of the transmission tree is being resampled). A value >0 requires a generator list whose type is unsampled.
starting.node	The root of the subtree to resample. If this is the root of the whole tree, then existing is irrelevent (but generally sample.tt should be used for this purpose).
existing	An existing list of class tt, representing a transmission tree to be modified. Usually these are produced by a sample.tt or sample.partial.tt call.
check.integrity	Whether to check if existing is indeed a valid transmission tree.
draw	Use ggtree to draw a coloured phylogeny showing each transmission tree overload onto the phylogeny
igraph	Produce the transmission trees in igraph format.
verbose	Verbose output

Value

A list, each of whose elements is a list of class tt with one or more of the following elements:

• annotations Always present. A vector indicating which host (given by numbers corresponding to the ordering in generator$hosts) is assigned to each phylogeny node.

• edgelist Always present. A data.frame giving the edge list; the first column are parents and the second children.

• hidden Present if unsampled is greater than 0. The number of "hidden" unsampled hosts (with no associated nodes) along each branch.

• picture Present if draw was TRUE; a ggtree object.

• igraph Present if igraph was TRUE; an igraph object.

Examples

# draw one sample from the uniform distribution
generator <- tt.generator(stratus.example.tree)
samples <- sample.tt(generator, 1, draw = TRUE)
original.tt <- samples[[1]]
# sample anew, from node 31 downwards
revised.tt <- sample.partial.tt(generator, 1, starting.node = 31, 
    existing = original.tt, draw = TRUE)

STraTUS documentation built on April 4, 2020, 5:07 p.m.