PhylogeneticEM (version 1.0.0)

simul_process: Simulate a Stochastic Process on a tree

Description

simulate simulate a stochastic process on a tree.

Usage

simul_process(x, ...)
"simul_process"(x, phylo, simulate_random = TRUE, checks = TRUE, U_tree = NULL, times_shared = NULL, ...)
"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 precised to avoid extra computations.

times_shared

optional, times of shared ancestry of all nodes and tips, result of function compute_times_ca. Can be precised to avoid extra computations.

Value

An S3 object of class simul_process. This contains:

Methods (by class)

• params_process: params_process object
• PhyloEM: PhyloEM object

See Also

params_process, PhyloEM