Convert intermediate output to final simulation output

Convert intermediate output to final simulation output

Usage

DAISIE_ONEcolonist(time, island_spec, stt_table)

Arguments

time

Numeric defining the length of the simulation in time units. For example, if an island is known to be 4 million years old, setting time = 4 will simulate the entire life span of the island; setting time = 2 will stop the simulation at the mid-life of the island.

island_spec

Matrix with current state of simulation containing number of species.

stt_table

Matrix with number of species at each time step.

Value

a list with these elements:

• [1]: stt_table, the same stt_table as put in.

• [2]: branching_times, a sorted numeric vector, as required by the ML estimation functions. The first element always refers to the island age. Subsequent elements refer to colonisation, speciation and recolonisation times. The most recent recolonisation time, if any is always omitted to approximate simulation results to the mathematical formulation of the likelihood functions used for MLE.

• [3]: stac, status of colonist. In this function it can be returned as either 2, 4 or 3. If stac is 2, then there is only one independent colonisation present on the island and the extant species are endemic. If stac is 4, then only a singleton endemic is present at the present. If stac is 3, then recolonisation occurred, and more than one colonising lineage.

• [4]: missing_species, a numeric value with the number of missing species, that is, species not sampled in the phylogeny but present on the island. As this code only runs for simulation models, here missing_species is always set to 0.

• [5]: all_colonisations, on recolonising lineages only. It is comprised of $event_times and $species_type:

  $event_times

  ordered numeric vectors containing all events for each extant recolonising lineage. This includes all colonisation and branching times. Each vector pertains to one colonising lineage.

  $species_type

  a string. Can be "A", "C" or "I" depending on whether the extant clade is of anagenetic, cladogenetic or immigrant origin, respectively.