Description Usage Arguments Value Examples
Resample the subtree rooted at any tree node, keeping the annotations for the rest of the tree fixed
1 2 3 4 5 6 7 8 9 10 11 | sample.partial.tt(
generator,
count = 1,
unsampled = 0,
starting.node = phangorn::getRoot(generator$tree),
existing = NULL,
check.integrity = TRUE,
draw = count == 1,
igraph = FALSE,
verbose = FALSE
)
|
generator |
A list of class |
count |
How many transmission trees to sample. |
unsampled |
The number of unsampled hosts in the transmission chain. (The whole transmission chain, even if only part of the transmission tree is being resampled). A value >0 requires a |
starting.node |
The root of the subtree to resample. If this is the root of the whole tree, then |
existing |
An existing list of class |
check.integrity |
Whether to check if |
draw |
Use |
igraph |
Produce the transmission trees in |
verbose |
Verbose output |
A list, each of whose elements is a list of class tt
with one or more of the following elements:
annotations
Always present. A vector indicating which host (given by numbers corresponding to the ordering in generator$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.
1 2 3 4 5 6 7 | # 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)
|
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