ts_tree: Get a tree from a given tree sequence

In bodkan/slendr: A Simulation Framework for Spatiotemporal Population Genetics

Get a tree from a given tree sequence

Description

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 zero-based indexing as in tskit), if mode = "position", a tree covering the i-th base of the simulated genome will be returned (again, in tskit's indexing).
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

init_env()

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

# load the tree-sequence object from disk
ts <- ts_read(slendr_ts, model)

# extract the zero-th tree in the tree sequence
tree <- ts_tree(ts, i = 0)

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

bodkan/slendr documentation built on Dec. 19, 2024, 11:41 p.m.