Convert a tree in the tree sequence to an object of the class phylo

Convert a tree in the tree sequence to an object of the class phylo

Usage

ts_phylo(
  ts,
  i,
  mode = c("index", "position"),
  labels = c("tskit", "pop"),
  quiet = FALSE
)

Arguments

ts: Tree sequence object of the class slendr_ts
i: Position of the tree in the tree sequence. If mode = "index", an i-th tree will be returned (in zero-based indexing as in tskit), if mode = "position", a tree covering the i-th base of the simulated genome will be returned (again, in tskit's indexing).
mode: How should the i argument be interpreted? Either "index" as an i-th tree in the sequence of genealogies, or "position" along the simulated genome.
labels: What should be stored as node labels in the final phylo object? Options are either a population name or a tskit integer node ID (which is a different thing from a phylo class node integer index).
quiet: Should ape's internal phylo validity test be printed out?

Value

Standard phylogenetic tree object implemented by the R package ape

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"))

# load the tree-sequence object from disk
ts <- ts_load(slendr_ts, model) %>%
  ts_recapitate(Ne = 10000, recombination_rate = 1e-8) %>%
  ts_simplify()

# extract the 1st tree from a given tree sequence, return ape object
tree <- ts_phylo(ts, i = 1, mode = "index", quiet = TRUE)
tree
#> 
#> Phylogenetic tree with 26 tips and 24 internal nodes.
#> 
#> Tip labels:
#>   25 (EUR_5), 24 (EUR_5), 23 (EUR_4), 22 (EUR_4), 21 (EUR_3), 20 (EUR_3), ...
#> Node labels:
#>   83, 28, 27, 30, 31, 32, ...
#> 
#> Rooted; includes branch lengths.

# extract the tree at a 42th basepair in the given tree sequence
tree <- ts_phylo(ts, i = 42, mode = "position", quiet = TRUE)

# because the tree is a standard ape phylo object, we can plot it easily
plot(tree, use.edge.length = FALSE)
ape::nodelabels()