sim.taxonomy

Simulate a taxonomy object relating species identity to a phylo object under a mixed model of speciation.
Anagenetic and cryptic species can also be added later using the <code>sim.anagenetic.species</code> and <code>sim.cryptic.species</code> functions.

Simulating and plotting taxonomy and fossil data on phylogenetic trees under mechanistic
models of speciation, preservation and sampling.

Joelle Barido-Sottani

FossilSim

Simulation and Plots for Fossil and Taxonomy Data

Rachel Warnock

Walker Pett

O'Reilly Joseph

Ugnė Stolz

sim.taxonomy function

<dl><dt>tree</dt>
<dd>Phylo object.</dd>
<dt>beta</dt>
<dd>Probability of bifurcating speciation. Default = 0.</dd>
<dt>lambda.a</dt>
<dd>Rate of anagenetic speciation. Default = 0.</dd>
<dt>kappa</dt>
<dd>Probability that speciation event is cryptic. Default = 0.</dd>
<dt>root.edge</dt>
<dd>If TRUE include root edge. Default = TRUE.</dd></dl>

Arguments

Simulate taxonomy — sim.taxonomy

<dl>

<dt>tree</dt>
<dd>Phylo object.</dd>


<dt>beta</dt>
<dd>Probability of bifurcating speciation. Default = 0.</dd>


<dt>lambda.a</dt>
<dd>Rate of anagenetic speciation. Default = 0.</dd>


<dt>kappa</dt>
<dd>Probability that speciation event is cryptic. Default = 0.</dd>


<dt>root.edge</dt>
<dd>If TRUE include root edge. Default = TRUE.</dd>

</dl>

sim.taxonomy: Simulate taxonomy

Description

Usage

Value

Arguments

See Also

Examples