init.simulate.StateAndExp

Function used in <code><a href="/link/simulate?package=PhylogeneticEM&version=1.8.0" data-mini-rdoc="PhylogeneticEM::simulate">simulate</a></code> for BM/OU initializations.

internal

Implementation of the automatic shift detection method for
Brownian Motion (BM) or Ornstein–Uhlenbeck (OU) models of trait evolution on
phylogenies. Some tools to handle equivalent shifts configurations are also
available. See Bastide et al. (2017) <doi:10.1111/rssb.12206> and
Bastide et al. (2018) <doi:10.1093/sysbio/syy005>.

Paul Bastide

PhylogeneticEM

Automatic Shift Detection using a Phylogenetic EM

Mahendra Mariadassou

init.simulate.StateAndExp function

<dl><dt>phy</dt>
<dd>Input tree.</dd>
<dt>p</dt>
<dd>dimension of the trait simulated</dd>
<dt>root.state</dt>
<dd>(list): state of the root, with:
random : random state (TRUE) or deterministic state (FALSE)
value.root : if deterministic, value of the character at the root
exp.root : if random, expectation of the character at the root
var.root : if random, variance of the character at the root (pxp matrix)</dd></dl>

Arguments

Function used in <code><a href='https://rdrr.io/r/stats/simulate.html'>simulate</a></code> for BM/OU initializations.

Initialize state and expectation matrices — init.simulate.StateAndExp

<dl>

<dt>phy</dt>
<dd>Input tree.</dd>


<dt>p</dt>
<dd>dimension of the trait simulated</dd>


<dt>root.state</dt>
<dd>(list): state of the root, with:
random : random state (TRUE) or deterministic state (FALSE)
value.root : if deterministic, value of the character at the root
exp.root : if random, expectation of the character at the root
var.root : if random, variance of the character at the root (pxp matrix)</dd>

</dl>

init.simulate.StateAndExp: Initialize state and expectation matrices

Description

Usage

Value

Arguments