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

Description Usage Arguments Value

View source: R/DAISIE_format_IW.R

Description

Formats island-wide simulation output into standard DAISIE list output

Usage

1
2
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 carrying capacity with trait state 2 on mainland

  • [8]: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/Trait_dependent_TraiSIE documentation built on Nov. 22, 2019, 7:51 a.m.