slendr (version 1.1.0)

ts_coalesced: 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)

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

Arguments

ts

Tree sequence object of the class slendr_ts

return_failed

Report back which trees failed the coalescence check?

Examples

check_dependencies(python = TRUE, quit = TRUE) # dependencies must be present

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)