R: Simulate a Stochastic Process on a tree

simul_process {PhylogeneticEM} | R Documentation

## 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 nNodes x 2 (BM) or p x nNodes 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)

- `params_process`: `params_process` object

- `PhyloEM`: `PhyloEM` object

### See Also

`params_process`, `PhyloEM`

[Package PhylogeneticEM version 1.1.0 Index]