brts2phylo

Converting a set of branching times to a phylogeny

models

Implements maximum likelihood and bootstrap methods based on
the diversity-dependent birth-death process to test whether
speciation or extinction are diversity-dependent, under various
models including various types of key innovations.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309,
<DOI:10.1098/rspb.2011.1439>,
Etienne & Haegeman 2012, Am. Nat. 180: E75-E89,
<DOI:10.1086/667574>,
Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099,
<DOI:10.1111/2041-210X.12565> and
Laudanno et al. 2021. Syst. Biol. 70: 389–407,
<DOI:10.1093/sysbio/syaa048>.
Also contains functions to simulate the diversity-dependent
process.

Rampal Etienne

Diversity-Dependent Diversification

Rampal S. Etienne

Bart Haegeman

Hanno Hildenbrandt

Giovanni Laudanno

brts2phylo function

<dl><dt>times</dt>
<dd>Set of branching times</dd>
<dt>root</dt>
<dd>When root is FALSE, the largest branching time will be assumed to be
the crown age. When root is TRUE, it will be the stem age.</dd>
<dt>tip.label</dt>
<dd>Tip labels. If set to NULL, the labels will be t1, t2, etc.</dd></dl>

Arguments

Author

Function to convert a set of branching times into a
phylogeny with random topology
This code is taken from the package TESS by Sebastian Hoehna, where the function
is called tess.create.phylo — brts2phylo

<dl>

<dt>times</dt>
<dd>Set of branching times</dd>


<dt>root</dt>
<dd>When root is FALSE, the largest branching time will be assumed to be
the crown age. When root is TRUE, it will be the stem age.</dd>


<dt>tip.label</dt>
<dd>Tip labels. If set to NULL, the labels will be t1, t2, etc.</dd>

</dl>

Function to convert a set of branching times into a
phylogeny with random topology
This code is taken from the package TESS by Sebastian Hoehna, where the function
is called tess.create.phylo

brts2phylo: Function to convert a set of branching times into a phylogeny with random topology This code is taken from the package TESS by Sebastian Hoehna, where the function is called tess.create.phylo

Description

Usage

Value

Arguments

Author

References