DAISIE_format_IW: Formats island-wide simulation output into standard DAISIE...

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

Description

Formats island-wide simulation output into standard DAISIE list output

Usage

DAISIE_format_IW(island_replicates, time, M, sample_freq,
  verbose = FALSE, Tpars = NULL, island_type = island_type)

Arguments

island_replicates	Island replicates in DAISIE format (produced in DAISIE_sim with format = TRUE option). Minimally, this must be a list, that has as much elements as replicates. Each element must be a list with the elements island_age, not_present and stt_all. stt_all must be a data frame with the column names Time, nI, nA, nC and present.
time	Length of the simulation in time units. For examples, 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.
M	The size of mainland pool, i.e. the number of species that can potentially colonize the island.
sample_freq	Specifies the number of units times should be divided by for plotting purposes. Larger values will lead to plots with higher resolution, but will also run slower.
verbose	sets whether parameters and likelihood should be printed (1) or not (0)
Tpars	A named list containing diversification rates considering two trait states: [1]:A numeric with the per capita transition rate with state1 [2]:A numeric with the per capita immigration rate with state2 [3]:A numeric with the per capita extinction rate with state2 [4]:A numeric with the per capita anagenesis rate with state2 [5]:A numeric with the per capita cladogenesis rate with state2 [6]:A numeric with the per capita transition rate with state2 [7]:A numeric with the number of species with trait state 2 on mainland
island_type	oceanic or non-oceanic island

Value

List with IW DAISIE simulation output

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