sse_states_to_endemicity

Convert SSE states back to endemicity status

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

sse_states_to_endemicity function

<dl><dt>states</dt>
<dd>integer vector of tip states, as expected by SSE models</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

Convert SSE states back to endemicity status — sse_states_to_endemicity

<dl>

<dt>states</dt>
<dd>integer vector of tip states, as expected by SSE models</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>

sse_states_to_endemicity: Convert SSE states back to endemicity status

Description

Usage

Value

Arguments