DAISIE_extract_stt_median

Extract the STT median from the output of DAISIE_sim functions

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

DAISIE_extract_stt_median function

<dl><dt>island_replicates</dt>
<dd>List output from
<code>DAISIE_sim_core_cr()</code>,
<code>DAISIE_sim_core_time_dep()</code>,
<code>DAISIE_sim_core_cr_shift()</code> or
<code>DAISIE_sim_min_type2()</code> functions. Minimally, this must be a
list that has as many elements as replicates. Each element must be a list
with the elements <code>island_age</code>, <code>not_present</code> and <code>stt_all</code>.
<code>stt_all</code> must be a data frame with the column names <code>Time</code>,
<code>nI</code>, <code>nA</code>, <code>nC</code> and <code>present</code>.</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

Extract the STT median from the output of DAISIE_sim functions — DAISIE_extract_stt_median

<dl>

<dt>island_replicates</dt>
<dd>List output from
<code>DAISIE_sim_core_cr()</code>,
<code>DAISIE_sim_core_time_dep()</code>,
<code>DAISIE_sim_core_cr_shift()</code> or
<code>DAISIE_sim_min_type2()</code> functions. Minimally, this must be a
list that has as many elements as replicates. Each element must be a list
with the elements <code>island_age</code>, <code>not_present</code> and <code>stt_all</code>.
<code>stt_all</code> must be a data frame with the column names <code>Time</code>,
<code>nI</code>, <code>nA</code>, <code>nC</code> and <code>present</code>.</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>

Extract the STT median from the output of DAISIE_sim functions

DAISIE_extract_stt_median: Extract the STT median from the output of DAISIE_sim functions

Description

Usage

Value

Arguments