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Simulate a phylogenetic tree from a birth-death-sampling process

Source: R/sim_bds_tree.R
sim_bds_tree.Rd

sim_bds_tree() simulates a phylogenetic tree with state annotations for all internal nodes and tips. A birth-death-sampling process is used to generate the tree topology and branch lengths; this will include speciation, sampling, and mutation events. A continuous-time Markov process is used to assign states to all nodes. The resulting tree will be compatible with saasi(). The tree is post-processed to remove tips at the present and ensure a minimum number of tips.

Usage

sim_bds_tree(
  params_df,
  q_matrix,
  x0,
  max_taxa = 100,
  max_t = 100,
  include_extinct = FALSE,
  min_tip = 1
)

Arguments

params_df

A data.frame specifying the parameters from which the tree will be simulated. Must contain

  • lambda: vector of speciation rates

  • mu: vector of extinction rates

  • psi: vector of sampling rates

The number of rows should be equal to the number of states.

q_matrix

State transition rate matrix.

x0

The root state.

max_taxa

Maximum number of nodes allowed in the initial simulated tree. Default value is 100.

max_t

Maximum depth allowed in the returned tree. Default value is 100.

include_extinct

Boolean. If TRUE, extinct taxa are included in the returned tree. Default value is FALSE.

min_tip

Minimum number of tips required in the post-processed tree. If the processed tree has fewer tips, the simulation is repeated until this condition is satisfied. Default value is 1.

Value

An object of class phylo that is compatible with saasi().

Examples

# Simulate a tree from the demo model with root state set to 1
demo_pars
#>   state rootprior lambda  mu psi
#> 1     1 0.3333333    1.5 0.3 0.1
#> 2     2 0.3333333    1.5 0.3 0.5
#> 3     3 0.3333333    1.5 0.3 0.5
demo_Q
#>      1    2    3
#> 1 -0.6  0.3  0.3
#> 2  0.3 -0.6  0.3
#> 3  0.3  0.3 -0.6
sim_bds_tree(demo_pars, demo_Q, 1)
#> 
#> Phylogenetic tree with 37 tips and 36 internal nodes.
#> 
#> Tip labels:
#>   sp1, sp2, sp3, sp4, sp5, sp6, ...
#> Node labels:
#>   nd1, nd2, nd9, nd14, nd19, nd20, ...
#> 
#> Rooted; includes branch length(s).