simul_process: Simulate a Stochastic Process on a tree

In pbastide/PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM

Simulate a Stochastic Process on a tree

Description

simulate simulate a stochastic process on a tree.

Usage

simul_process(x, ...)

## S3 method for class 'params_process'
simul_process(
  x,
  phylo,
  simulate_random = TRUE,
  checks = TRUE,
  U_tree = NULL,
  times_shared = NULL,
  ...
)

## S3 method for class 'PhyloEM'
simul_process(
  x,
  simulate_random = TRUE,
  checks = TRUE,
  U_tree = NULL,
  times_shared = NULL,
  ...
)

Arguments

x	an object of class params_process or PhyloEM.
...	for a PhyloEM object, further arguments to be passed on to params_process.PhyloEM (to choose which parameters to extract from the results, see documentation of this function).
phylo	a phylogenetic tree, class phylo.
simulate_random	set to FALSE if only the expected values are needed (and not the random sample). Default to TRUE.
checks	whether to check the entry parameters for consistency. Default to TRUE.
U_tree	optional, full incidence matrix of the tree, result of function incidence.matrix.full. Can be specified to avoid extra computations.
times_shared	optional, times of shared ancestry of all nodes and tips, result of function compute_times_ca. Can be specified to avoid extra computations.

Value

An S3 object of class simul_process. This contains:

sim_traits

an array with dimensions p x Nnode x 2 (BM) or p x Nnode x 3 (OU). For each trait t, 1 <= t <= p, sim_traits[t, , ] has tree columns, containing respectively the simulated state, expected value and optimal value for all the nodes.

phylo

the phylogenetic tree used for the simulations (class phylo).

params

the parameters used for the simulations (class params_proces).

Methods (by class)

• simul_process(params_process): params_process object

• simul_process(PhyloEM): PhyloEM object

See Also

params_process, PhyloEM, extract.simul_process

pbastide/PhylogeneticEM documentation built on Feb. 12, 2024, 1:27 a.m.