Recapitate the tree sequence

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

Arguments

ts

Tree sequence object loaded by ts_load

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

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

check_dependencies(python = TRUE) # make sure dependencies are present

# load an example model with an already simulated tree sequence
slendr_ts <- system.file("extdata/models/introgression.trees", package = "slendr")
model <- read_model(path = system.file("extdata/models/introgression", package = "slendr"))

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

ts
#> ╔════════════════════════╗
#> ║TreeSequence            ║
#> ╠═══════════════╤════════╣
#> ║Trees          │      24║
#> ╟───────────────┼────────╢
#> ║Sequence Length│  500000║
#> ╟───────────────┼────────╢
#> ║Time Units     │   ticks║
#> ╟───────────────┼────────╢
#> ║Sample Nodes   │      26║
#> ╟───────────────┼────────╢
#> ║Total Size     │58.1 KiB║
#> ╚═══════════════╧════════╝
#> ╔═══════════╤════╤════════╤════════════╗
#> ║Table      │Rows│Size    │Has Metadata║
#> ╠═══════════╪════╪════════╪════════════╣
#> ║Edges      │ 133│ 4.2 KiB│          No║
#> ╟───────────┼────┼────────┼────────────╢
#> ║Individuals│  55│ 7.2 KiB│         Yes║
#> ╟───────────┼────┼────────┼────────────╢
#> ║Migrations │   0│ 8 Bytes│          No║
#> ╟───────────┼────┼────────┼────────────╢
#> ║Mutations  │   0│ 1.2 KiB│          No║
#> ╟───────────┼────┼────────┼────────────╢
#> ║Nodes      │  68│ 3.2 KiB│         Yes║
#> ╟───────────┼────┼────────┼────────────╢
#> ║Populations│   5│ 2.6 KiB│         Yes║
#> ╟───────────┼────┼────────┼────────────╢
#> ║Provenances│   3│36.1 KiB│          No║
#> ╟───────────┼────┼────────┼────────────╢
#> ║Sites      │   0│16 Bytes│          No║
#> ╚═══════════╧════╧════════╧════════════╝
#>