sample.tt: Sample one or more transmission trees uniformly

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

Description

Sample one or more transmission trees uniformly

Usage

sample.tt(
  generator,
  count = 1,
  unsampled = 0,
  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.
draw	Use ggtree to draw a coloured phylogeny showing each transmission tree overlaid 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)
samples[[1]]
# with unsampled.hosts
generator.us <- tt.generator(stratus.example.tree, max.unsampled = 2)
# note that you can ask for less unsampled hosts than the generator has (but not more)
samples.1us <- sample.tt(generator.us, 1, unsampled = 1,  draw = TRUE)
samples.1us[[1]]
# with multiply sampled hosts
generator.ms <- tt.generator(stratus.example.tree, tip.map = grouping.map)
samples.ms <- sample.tt(generator.ms, 1, draw = TRUE)

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