get_sse_tip_states

Extract tip states from a phylod object

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

get_sse_tip_states 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>sse_model</dt>
<dd>either "musse" (default) or "geosse". MuSSE expects state
values 1, 2, 3, which here we encode as "not_present", "endemic",
"nonendemic", respectively. GeoSSE expects trait values 0, 1, 2, with 0 the
widespread state (here, "nonendemic"), and 1 and 2 are "not_present" and
"endemic", respectively.</dd></dl>

Arguments

Extract tip states from a phylod object — get_sse_tip_states

<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>sse_model</dt>
<dd>either "musse" (default) or "geosse". MuSSE expects state
values 1, 2, 3, which here we encode as "not_present", "endemic",
"nonendemic", respectively. GeoSSE expects trait values 0, 1, 2, with 0 the
widespread state (here, "nonendemic"), and 1 and 2 are "not_present" and
"endemic", respectively.</dd>

</dl>

get_sse_tip_states: Extract tip states from a phylod object

Description

Usage

Value

Arguments