L2brts

Converting a table with speciation and extinction events to a set of
branching times

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

L2brts function

<dl><dt>L</dt>
<dd>Matrix of events as produced by dd_sim: - the first column
is the time at which a species is born in Mya - the second column is the
label of the parent of the species; positive and negative values indicate
whether the species belongs to the left or right crown lineage - the
third column is the label of the daughter species itself; positive and
negative values indicate whether the species belongs to the left or right
crown lineage - the fourth column is the time of extinction of the
species; if the fourth element equals -1, then the species is still extant.</dd>
<dt>dropextinct</dt>
<dd>Sets whether the phylogeny should drop species that are
extinct at the present</dd></dl>

Arguments

Author

Function to convert a table with speciation and extinction events to a set
of branching times — L2brts

<dl>

<dt>L</dt>
<dd>Matrix of events as produced by dd_sim: - the first column
is the time at which a species is born in Mya - the second column is the
label of the parent of the species; positive and negative values indicate
whether the species belongs to the left or right crown lineage - the
third column is the label of the daughter species itself; positive and
negative values indicate whether the species belongs to the left or right
crown lineage - the fourth column is the time of extinction of the
species; if the fourth element equals -1, then the species is still extant.</dd>


<dt>dropextinct</dt>
<dd>Sets whether the phylogeny should drop species that are
extinct at the present</dd>

</dl>

L2brts: Function to convert a table with speciation and extinction events to a set of branching times

Description

Usage

Value

Arguments

Author

References

Examples