create_full_CS_stt

internal

Simulates and computes the (maximum) likelihood of a dynamical
model of island biota assembly through speciation, immigration and
extinction. See Valente et al. (2015) <doi:10.1111/ele.12461>.

Rampal Etienne

DAISIE

Dynamical Assembly of Islands by Speciation, Immigration and
Extinction

Rampal S. Etienne

Luis Valente

Albert B. Phillimore

Bart Haegeman

Joshua W. Lambert

Pedro Santos Neves

Shu Xie

Richèl J.C. Bilderbeek

Hanno Hildenbrandt

Torsten Hauffe

Giovanni Laudanno

Nadiah Kristensen

Raphael Scherrer

create_full_CS_stt function

<dl><dt>stt_list</dt>
<dd>List of full stt tables as
returned by DAISIE_sim_core functions</dd>
<dt>stac_vec</dt>
<dd>Vector with status of species on island.</dd>
<dt>total_time</dt>
<dd>Numeric double with total time of simulation.</dd>
<dt>trait_pars</dt>
<dd>A named list containing diversification rates considering
two trait states created by <code>create_trait_pars</code>:<ul>
<li>[1]:A numeric with the per capita transition rate with state1</li>
<li>[2]:A numeric with the per capita immigration rate with state2</li>
<li>[3]:A numeric with the per capita extinction rate with state2</li>
<li>[4]:A numeric with the per capita anagenesis rate with state2</li>
<li>[5]:A numeric with the per capita cladogenesis rate with state2</li>
<li>[6]:A numeric with the per capita transition rate with state2</li>
<li>[7]:A numeric with the number of species with trait state 2 on
 mainland</li>
</ul></dd></dl>

Arguments

Pedro Neves, Joshua Lambert, Shu Xie, Giovanni Laudanno

Author

Unsampled CS full STT — create_full_CS_stt

<dl>

<dt>stt_list</dt>
<dd>List of full stt tables as
returned by DAISIE_sim_core functions</dd>


<dt>stac_vec</dt>
<dd>Vector with status of species on island.</dd>


<dt>total_time</dt>
<dd>Numeric double with total time of simulation.</dd>


<dt>trait_pars</dt>
<dd>A named list containing diversification rates considering
two trait states created by <code>create_trait_pars</code>:<ul>
<li>[1]:A numeric with the per capita transition rate with state1</li>
<li>[2]:A numeric with the per capita immigration rate with state2</li>
<li>[3]:A numeric with the per capita extinction rate with state2</li>
<li>[4]:A numeric with the per capita anagenesis rate with state2</li>
<li>[5]:A numeric with the per capita cladogenesis rate with state2</li>
<li>[6]:A numeric with the per capita transition rate with state2</li>
<li>[7]:A numeric with the number of species with trait state 2 on
 mainland</li>
</ul></dd>

</dl>

Unsampled CS full STT

create_full_CS_stt: Unsampled CS full STT

Description

Usage

Value

Arguments

Author