extract_asr_clade

Extracts an island clade based on the ancestral state reconstruction of the
species presence on the island, therefore this clade can contain
non-endemic species as well as endemic species.

Extracts colonisation and branching times of island
species to be used for analysis in the R package 'DAISIE'. It uses
phylogenetic and endemicity data to extract the separate island colonists
and store them.

Joshua W. Lambert

DAISIEprep

Extracts Phylogenetic Island Community Data from Phylogenetic
Trees

Luis Valente

Pedro Santos Neves

Lizzie Roeble

Theo Pannetier

extract_asr_clade function

<dl><dt>phylod</dt>
<dd>A <code>phylo4d</code> object from the package <code>phylobase</code> containing
phylogenetic and endemicity data for each species.</dd>
<dt>species_label</dt>
<dd>The tip label of the species of interest.</dd>
<dt>clade</dt>
<dd>A numeric vector which the indices of the species which are
in the island clade.</dd>
<dt>include_not_present</dt>
<dd>A boolean determining whether species not present
on the island should be included in island colonist when embedded within an
island clade. Default is FALSE.</dd></dl>

Arguments

Extracts an island clade based on the ancestral state reconstruction of the
species presence on the island, therefore this clade can contain
non-endemic species as well as endemic species. — extract_asr_clade

<dl>

<dt>phylod</dt>
<dd>A <code>phylo4d</code> object from the package <code>phylobase</code> containing
phylogenetic and endemicity data for each species.</dd>


<dt>species_label</dt>
<dd>The tip label of the species of interest.</dd>


<dt>clade</dt>
<dd>A numeric vector which the indices of the species which are
in the island clade.</dd>


<dt>include_not_present</dt>
<dd>A boolean determining whether species not present
on the island should be included in island colonist when embedded within an
island clade. Default is FALSE.</dd>

</dl>

Extracts an island clade based on the ancestral state reconstruction of the
species presence on the island, therefore this clade can contain
non-endemic species as well as endemic species.

extract_asr_clade: Extracts an island clade based on the ancestral state reconstruction of the species presence on the island, therefore this clade can contain non-endemic species as well as endemic species.

Description

Usage

Value

Arguments