ProcessSimSample

Takes output from <code>GetFossils</code> and places extinct lineages in the tree and produces a properly formatted table of fossil samples from lineages that survive to the present (k fossils).

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

ProcessSimSample function

<dl><dt>phy</dt>
<dd>a complete phylogeny that includes both extant and extinct lineages.</dd>
 
<dt>f</dt>
<dd>the table of sampled lineages under the fossilized birth-death process obtained from <code>GetFossils</code>.</dd></dl>

Arguments

Process fossilized birth-death sample of lineages — ProcessSimSample

<dl>

<dt>phy</dt>
<dd>a complete phylogeny that includes both extant and extinct lineages.</dd>
 
<dt>f</dt>
<dd>the table of sampled lineages under the fossilized birth-death process obtained from <code>GetFossils</code>.</dd>

</dl>

ProcessSimSample: Process fossilized birth-death sample of lineages

Description

Usage

Value

Arguments