AddStratIntervals

Takes a sampled set of stratigraphic intervals from <code>GeteStratigraphicIntervals</code> and adds them as segments to a plot of the phylogeny from which they were sampled.

plotting

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

AddStratIntervals 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><dt>...</dt>
<dd>Additional parameters to control the points. See <code>segments</code>.</dd></dl>

Arguments

Author

Adds sampled stratigraphic intervals to a complete phylogeny — AddStratIntervals

<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>

<dt>...</dt>
<dd>Additional parameters to control the points. See <code>segments</code>.</dd>

</dl>

AddStratIntervals: Adds sampled stratigraphic intervals to a complete phylogeny

Description

Usage

Arguments

Author

References