estimate.alpha

<code>optimize</code> to maximize the
conditional expectation log likelihood in alpha. The interval is
set to [alpha_old/2, 2*alpha_old], supposing that the previous guess of 
alpha_old is not far from reality.

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

estimate.alpha function

<dl><dt>phylo</dt>
<dd>Input tree.</dd>
<dt>conditional_law_X</dt>
<dd>result of function <code>compute_E.OU</code></dd>
<dt>sigma2</dt>
<dd>variance of params</dd>
<dt>mu</dt>
<dd>mean of the root state</dd>
<dt>shifts</dt>
<dd>list of shifts on the tree</dd>
<dt>alpha_old</dt>
<dd>previous estimation of the selection strength</dd>
<dt>max_selection.strength</dt>
<dd>the maximal value of alpha authorized by
the user</dd></dl>

Arguments

Function to estimate alpha — estimate.alpha

<dl>

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


<dt>conditional_law_X</dt>
<dd>result of function <code>compute_E.OU</code></dd>


<dt>sigma2</dt>
<dd>variance of params</dd>


<dt>mu</dt>
<dd>mean of the root state</dd>


<dt>shifts</dt>
<dd>list of shifts on the tree</dd>


<dt>alpha_old</dt>
<dd>previous estimation of the selection strength</dd>


<dt>max_selection.strength</dt>
<dd>the maximal value of alpha authorized by
the user</dd>

</dl>

estimate.alpha: Function to estimate alpha

Description

Usage

Value

Arguments

Details