Extend the span of sequences covered by ancestral nodes (EXPERIMENTAL)

Run the "extend haplotypes" algorithm to extend the span of sequence covered by ancestral nodes, as implemented by the tskit method TreeSequence.extend_haplotypes.

Usage

ts_extend(ts, iterations = 10)

Arguments

ts: Tree sequence object
iterations: Maximum number of iterations over the tree sequence (default is 10)

Value

Tree-sequence object of the class slendr_ts

Details

For more details about this functionality, please read the following resources:

Paper by Fritze et al. 2025 (doi:10.1093/genetics/iyaf198 )
Official tskit documentation at https://tskit.dev/tskit/docs/stable/python-api.html#tskit.TreeSequence.extend_haplotypes

Note that this function has been currently tested exclusively on tree sequences simulated by slendr's msprime() simulation engine.

Examples

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_msprime.trees", package = "slendr")
model <- read_model(path = system.file("extdata/models/introgression", package = "slendr"))

ts <- ts_read(slendr_ts, model)
ts_ext <- ts_extend(ts, iterations = 10)

ts_ext
#> ╔═══════════════════════════╗
#> ║TreeSequence               ║
#> ╠═══════════════╤═══════════╣
#> ║Trees          │        180║
#> ╟───────────────┼───────────╢
#> ║Sequence Length│  1,000,000║
#> ╟───────────────┼───────────╢
#> ║Time Units     │generations║
#> ╟───────────────┼───────────╢
#> ║Sample Nodes   │         26║
#> ╟───────────────┼───────────╢
#> ║Total Size     │   37.7 KiB║
#> ╚═══════════════╧═══════════╝
#> ╔═══════════╤════╤═════════╤════════════╗
#> ║Table      │Rows│Size     │Has Metadata║
#> ╠═══════════╪════╪═════════╪════════════╣
#> ║Edges      │ 621│ 19.4 KiB│          No║
#> ╟───────────┼────┼─────────┼────────────╢
#> ║Individuals│  13│388 Bytes│          No║
#> ╟───────────┼────┼─────────┼────────────╢
#> ║Migrations │   0│  8 Bytes│          No║
#> ╟───────────┼────┼─────────┼────────────╢
#> ║Mutations  │   0│ 16 Bytes│          No║
#> ╟───────────┼────┼─────────┼────────────╢
#> ║Nodes      │ 339│  9.3 KiB│          No║
#> ╟───────────┼────┼─────────┼────────────╢
#> ║Populations│   4│338 Bytes│         Yes║
#> ╟───────────┼────┼─────────┼────────────╢
#> ║Provenances│   1│  2.8 KiB│          No║
#> ╟───────────┼────┼─────────┼────────────╢
#> ║Sites      │   0│ 16 Bytes│          No║
#> ╚═══════════╧════╧═════════╧════════════╝
#>