| stac_table {DAISIE} | R Documentation |
Explanatory table on meaning and use of stac settings
Description
A table containing the information regarding the meaning
of the stac codes utilised by DAISIE's ML functions. It is used to
render the "DAISIE stac values" vignette.
stac stands for "status of the clade" formed by the immigrant. It is
an important part of DAISIE objects that informs the likelihood functions
about the endemicity status and type of data available for each insular
clade. Each colonisation event that has extant species on the island needs to
have a stac value specified. This also has implications in what is
included in the DAISIE object "branching_times" vector, which also
described in this table.
The table is composed of the following columns:
$stac: A numeric with each stac code from 1 until 9.
$Input for DAISIE_dataprep table "Clade_Name": A character with the possibilities for input in DAISIE_dataprep() of each clade, which are then translated to a numeric
staccode as in$stac.$Type of species or clade": A character with the plain English explanation of the different possible kinds of island lineages that can be considered by DAISIE.
$Input for DAISIE_dataprep table "Branching_times": A character with the plain English explanation of what the branching times vector in the DAISIE object should contain.
$Colonisation times: A character with the plain English explanation of what the colonisation time in the branching times vector of the DAISIE object (first element of the vector) means.
Format
A table with 9 rows and 5 columns.