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Recapitate the tree sequence

Source: R/tree-sequences.R
ts_recapitate.Rd

Recapitate the tree sequence

Usage

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

Arguments

ts

Tree sequence object loaded by ts_read

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 (if NULL, a seed will be generated between 0 and the maximum integer number available)

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, quit = TRUE) # dependencies must be present

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

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

ts
#> ╔════════════════════════╗
#> ║TreeSequence            ║
#> ╠═══════════════╤════════╣
#> ║Trees          │      68║
#> ╟───────────────┼────────╢
#> ║Sequence Length│  500000║
#> ╟───────────────┼────────╢
#> ║Time Units     │   ticks║
#> ╟───────────────┼────────╢
#> ║Sample Nodes   │      26║
#> ╟───────────────┼────────╢
#> ║Total Size     │77.5 KiB║
#> ╚═══════════════╧════════╝
#> ╔═══════════╤════╤════════╤════════════╗
#> ║Table      │Rows│Size    │Has Metadata║
#> ╠═══════════╪════╪════════╪════════════╣
#> ║Edges      │ 294│ 9.2 KiB│          No║
#> ╟───────────┼────┼────────┼────────────╢
#> ║Individuals│  71│ 8.7 KiB│         Yes║
#> ╟───────────┼────┼────────┼────────────╢
#> ║Migrations │   0│ 8 Bytes│          No║
#> ╟───────────┼────┼────────┼────────────╢
#> ║Mutations  │   0│ 1.2 KiB│          No║
#> ╟───────────┼────┼────────┼────────────╢
#> ║Nodes      │  85│ 3.8 KiB│         Yes║
#> ╟───────────┼────┼────────┼────────────╢
#> ║Populations│   6│ 2.7 KiB│         Yes║
#> ╟───────────┼────┼────────┼────────────╢
#> ║Provenances│   4│46.9 KiB│          No║
#> ╟───────────┼────┼────────┼────────────╢
#> ║Sites      │   0│16 Bytes│          No║
#> ╚═══════════╧════╧════════╧════════════╝
#>