phylogenetic_diversity

The phylogenetic diversity at time t is given by the total
branch length of the tree reconstructed up until time point t. Time is
measured increasingly, with the crown age equal to 0. Thus, the time at
the present is equal to the crown age.

Collection of phylogenetic tree statistics,
collected throughout the literature. All functions have been
written to maximize computation speed. The package includes
umbrella functions to calculate all statistics, all balance
associated statistics, or all branching time related statistics.
Furthermore, the 'treestats' package supports summary statistic
calculations on Ltables, provides speed-improved coding of
branching times, Ltable conversion and includes algorithms to
create intermediately balanced trees. Full description can be
found in Janzen (2024) <doi:10.1016/j.ympev.2024.108168>.

Thijs Janzen

treestats

Phylogenetic Tree Statistics

phylogenetic_diversity function

<dl><dt>input_obj</dt>
<dd>phylo object or Ltable</dd>
<dt>t</dt>
<dd>time point at which to measure phylogenetic diversity, alternatively
a vector of time points can also be provided. Time is measured with 0 being
the present.</dd>
<dt>extinct_tol</dt>
<dd>tolerance to determine if a lineage is extinct at time t.
Default is 1/100 * smallest branch length of the tree.</dd></dl>

Arguments

Phylogenetic diversity at time point t — phylogenetic_diversity

<dl>

<dt>input_obj</dt>
<dd>phylo object or Ltable</dd>


<dt>t</dt>
<dd>time point at which to measure phylogenetic diversity, alternatively
a vector of time points can also be provided. Time is measured with 0 being
the present.</dd>


<dt>extinct_tol</dt>
<dd>tolerance to determine if a lineage is extinct at time t.
Default is 1/100 * smallest branch length of the tree.</dd>

</dl>

phylogenetic_diversity: Phylogenetic diversity at time point t

Description

Usage

Value

Arguments

References