create_mu_vector

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

create_mu_vector function

<dl><dt>state_names</dt>
<dd>vector of names of all 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>model</dt>
<dd>used model, choice of <code>"ETD"</code> (Examined Traits Diversification),
<code>"CTD"</code> (Concealed Traits Diversification) or <code>"CR"</code> (Constant Rate).</dd>
<dt>lambda_list</dt>
<dd>previously generated list of lambda matrices,
used to infer the rate number to start with.</dd></dl>

Arguments

Generate mus vector — create_mu_vector

<dl>

<dt>state_names</dt>
<dd>vector of names of all 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>model</dt>
<dd>used model, choice of <code>"ETD"</code> (Examined Traits Diversification),
<code>"CTD"</code> (Concealed Traits Diversification) or <code>"CR"</code> (Constant Rate).</dd>


<dt>lambda_list</dt>
<dd>previously generated list of lambda matrices,
used to infer the rate number to start with.</dd>

</dl>

Generate mus vector

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create_mu_vector: Generate mus vector

Description

Usage

Value

Arguments