ts_coalesced: Check that all trees in the tree sequence are fully coalesced

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

Check that all trees in the tree sequence are fully coalesced

Description

Check that all trees in the tree sequence are fully coalesced

Usage

ts_coalesced(ts, return_failed = FALSE)

Arguments

ts	Tree sequence object of the class slendr_ts
return_failed	Report back which trees failed the coalescence check?

Value

TRUE or FALSE value if return_failed = FALSE, otherwise a vector of (tskit Python 0-based) indices of trees which failed the coalescence test

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)

ts_coalesced(ts) # is the tree sequence fully coalesced? (TRUE or FALSE)

# returns a vector of tree sequence segments which are not coalesced
not_coalesced <- ts_coalesced(ts, return_failed = TRUE)

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