Extract source-population ancestry intervals — tskit_ancestry

For every focal sample and marginal tree, this function walks toward the root and records the first node whose population is one of source_populations. Adjacent tree intervals with the same source are merged. This is exact ancestry truth only when the simulation's population and node-retention semantics make those source populations authoritative.

Usage

tskit_ancestry_intervals(
  x,
  source_populations,
  samples = NULL,
  require_resolved = TRUE
)

Arguments

x: A TreeSequence.
source_populations: A non-empty vector of zero-based source-population IDs. Names, when supplied, become the returned source labels and should be dataset-qualified.
samples: Zero-based focal sample-node IDs. NULL uses every sample.
require_resolved: Whether to fail if a focal lineage reaches a root without encountering a declared source population.

Value

A data frame of sample IDs, half-open intervals, source labels, and source-population IDs, grouped by sample and ordered by coordinate.

References

Haller et al. (2019), Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes, doi:10.1111/1755-0998.12968 . The published local-ancestry example is pinned at SLiMTreeSeqPub commit 6715c28b02942bc4757c9f8bcab133ad4a0bfcfb.