expand_q_matrix

Function to expand an existing q_matrix to a number of concealed states

Simultaneously infers state-dependent diversification across
two or more states of a single or multiple traits while accounting for the
role of a possible concealed trait. See Herrera-Alsina et al. (2019)
<doi:10.1093/sysbio/syy057>.

Rampal Etienne

secsse

Several Examined and Concealed States-Dependent Speciation and
Extinction

Leonel Herrera Alsina

Paul van Els

Thijs Janzen

Hanno Hildenbrandt

Pedro Santos Neves

Rampal S. Etienne

expand_q_matrix function

<dl><dt>q_matrix</dt>
<dd><code>q_matrix</code> with only transitions between observed states.</dd>
<dt>num_concealed_states</dt>
<dd>number of concealed states, generally equivalent
to the number of examined states in the dataset.</dd>
<dt>diff.conceal</dt>
<dd>Boolean stating if the concealed states should be
different. E.g. that the transition rates for the concealed
states are different from the transition rates for the examined states.
Normally it should be <code>FALSE</code> in order to avoid having a huge number of
parameters.</dd></dl>

Arguments

Function to expand an existing q_matrix to a number of concealed states — expand_q_matrix

<dl>

<dt>q_matrix</dt>
<dd><code>q_matrix</code> with only transitions between observed states.</dd>


<dt>num_concealed_states</dt>
<dd>number of concealed states, generally equivalent
to the number of examined states in the dataset.</dd>


<dt>diff.conceal</dt>
<dd>Boolean stating if the concealed states should be
different. E.g. that the transition rates for the concealed
states are different from the transition rates for the examined states.
Normally it should be <code>FALSE</code> in order to avoid having a huge number of
parameters.</dd>

</dl>

expand_q_matrix: Function to expand an existing q_matrix to a number of concealed states

Description

Usage

Value

Arguments