Get a tree from a given tree sequence

For more information about optional keyword arguments see tskit documentation: https://tskit.dev/tskit/docs/stable/python-api.html#the-treesequence-class

Usage

ts_tree(ts, i, mode = c("index", "position"), ...)

Arguments

ts: Tree sequence object of the class slendr_ts
i: Position of the tree in the tree sequence. If mode = "index", an i-th tree will be returned (in one-based indexing), if mode = "position", a tree covering an i-th base of the simulated genome will be returned.
mode: How should the i argument be interpreted? Either "index" as an i-th tree in the sequence of genealogies, or "position" along the simulated genome.
...: Additional keyword arguments accepted by tskit.TreeSequence.at and tskit.TreeSequence.at_index methods

Value

Python-reticulate-based object of the class tskit.trees.Tree

Examples

check_dependencies(python = TRUE) # make sure dependencies are present

init_env()
#> The interface to all required Python modules has been activated.

# load an example model with an already simulated tree sequence
slendr_ts <- system.file("extdata/models/introgression.trees", package = "slendr")
model <- read_model(path = system.file("extdata/models/introgression", package = "slendr"))

# load the tree-sequence object from disk
ts <- ts_load(slendr_ts, model, simplify = TRUE)

# extract the first tree in the tree sequence
tree <- ts_tree(ts, i = 1)

# extract the tree at a position 100000bp in the tree sequence
tree <- ts_tree(ts, i = 100000, mode = "position")