plot_daisie_data: Plot the 'daisie_data'.
In joshwlambert/DAISIEmainland: Simulates Data for Phylogenetic Data on Islands for DAISIE with the Addition of Mainland Dynamics

plot_daisie_data

R Documentation

Plot the `daisie_data`.

Description

Plot the daisie_data.

Usage

plot_daisie_data(daisie_data)

Arguments

daisie_data

a DAISIE datalist, as can be checked by check_daisie_data. To quote the DAISE doc:

A datalist is an object containing information on colonisation and branching times. This object can be generated using DAISIE_dataprep, which converts a user-specified data table into a datalist, but the object can of course also be entered directly.

A datalist is a list with the following elements:

The first element of the list has two or three components:

$island_age - the island age

Then, depending on whether a distinction between types is made, we have:

$not_present - the number of mainland lineages that are not present on the island

or:

$not_present_type1 - the number of mainland lineages of type 1 that are not present on the island
$not_present_type2 - the number of mainland lineages of type 2 that are not present on the island

The remaining elements of the datalist each contains information on a single colonist lineage on the island and has 5 components:

$colonist_name - the name of the species or clade that colonized the island
$branching_times - island age followed by stem age of the population/species in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close relatives on the island. For endemic clades with more than one species on the island (cladogenetic clades/ radiations) these should be island age followed by the branching times of the island clade including the stem age of the clade
$stac - the status of the colonist, see stac_to_str for values and descriptions
$missing_species - number of island species that were not sampled for particular clade (only applicable for endemic clades)
$type1or2 - whether the colonist belongs to type 1 or type 2

Details

Each colonisation and re-colonisation event has its own branching dynamics. For clades that start from anagenesis, these are marked as such, until their first cladogenesis event. Due to this, it may seem that anagenetic clades do not speciate, but this is false: they are plotted as such until a (cladegenetic) speciation event.