GetFossils

Samples a simulated tree of extinct and extant lineages according to the preservation rate of the fossilized birth-death process.

Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification. Beaulieu and O'Meara (2016) <doi:10.1093/sysbio/syw022>.

Jeremy Beaulieu

hisse

Hidden State Speciation and Extinction

Brian O'Meara

Daniel Caetano

James Boyko

Thais Vasconcelos

GetFossils function

<dl><dt>phy</dt>
<dd>a complete phylogeny that includes both extant and extinct lineages.</dd>
 
<dt>psi</dt>
<dd>the preservation rate for which lineages will be sampled under a fossilized birth-death process.</dd></dl>

Arguments

Get fossilized birth-death samples — GetFossils

<dl>

<dt>phy</dt>
<dd>a complete phylogeny that includes both extant and extinct lineages.</dd>
 
<dt>psi</dt>
<dd>the preservation rate for which lineages will be sampled under a fossilized birth-death process.</dd>

</dl>

GetFossils: Get fossilized birth-death samples

Description

Usage

Value

Arguments