ts_recapitate: Recapitate the tree sequence

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

Recapitate the tree sequence

Description

Recapitate the tree sequence

Usage

ts_recapitate(
  ts,
  recombination_rate,
  Ne = NULL,
  demography = NULL,
  random_seed = NULL
)

Arguments

ts	Tree sequence object loaded by ts_read
recombination_rate	A constant value of the recombination rate
Ne	Effective population size during the recapitation process
demography	Ancestral demography to be passed internally to msprime.sim_ancestry() (see msprime's documentation for mode detail)
random_seed	Random seed passed to pyslim's recapitate method (if NULL, a seed will be generated between 0 and the maximum integer number available)

Value

Tree-sequence object of the class slendr_ts, which serves as an interface point for the Python module tskit using slendr functions with the ts_ prefix.

See Also

ts_nodes for extracting useful information about individuals, nodes, coalescent times and geospatial locations of nodes on a map

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"))

ts <- ts_read(slendr_ts, model) %>%
  ts_recapitate(recombination_rate = 1e-8, Ne = 10000, random_seed = 42)

ts

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