islands_1type_1000reps: 1000 islands in DAISIE format simulated with the ML...

In xieshu95/Test-Trasie: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Description

Each simulated dataset is an element of the list, which can be called using e.g. islands_1type_1000reps[[1]] Each of the island replicates is a list in itself. The first (e.g. islands_1type_1000reps[[x]][[1]]) element of that list has the following components:
$island_age - the island age
$not_present - the number of mainland lineages that are not present on the island
$stt_all - STT table for all species on the island (nI - number of non-endemic species; nA - number of anagenetic species, nC - number of cladogenetic species, present - number of independent colonisations present )
The subsequent elements of the list each contain information on a single colonist lineage on the island and has 3 components:
$branching_times - island age and stem age of the population/species in the case of Non-endemic, Non-endemic_MaxAge and Endemic anagenetic species. For cladogenetic species these should be island age and branching times of the radiation including the stem age of the radiation.
$stac - the status of the colonist
* Non_endemic_MaxAge: 1
* Endemic: 2
* Endemic&Non_Endemic: 3
* Non_endemic: 4
$missing_species - number of island species that were not sampled for particular clade (only applicable for endemic clades)

Format

A list with 1000 items.

Source

Valente, L.M., A.B. Phillimore and R.S. Etienne (2015). Equilibrium and non-equilibrium dynamics simultaneously operate in the Galapagos islands. Ecology Letters 18: 844-852.

See Also

DAISIE_sim, DAISIE_plot_sims

xieshu95/Test-Trasie documentation built on Dec. 18, 2019, 7:34 a.m.