DAISIE_format_CS_sampled_stt: Formats clade-specific simulation output into standard DAISIE...
In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

View source: R/DAISIE_format_CS_sampled_stt.R

Formats clade-specific simulation output into standard DAISIE list output

DAISIE_format_CS_sampled_stt(
  island_replicates,
  time,
  M,
  sample_freq,
  verbose = TRUE,
  trait_pars = NULL
)

`island_replicates`	List output from `DAISIE_sim_core_constant_rate()`, `DAISIE_sim_core_time_dependent()`, `DAISIE_sim_core_constant_rate_shift()` or `DAISIE_sim_min_type2()` functions. Minimally, this must be a list that has as many 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`	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.
`M`	Numeric defining the size of mainland pool, i.e. the number of species that can potentially colonize the island.
`sample_freq`	Numeric specifing 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`	In simulation and dataprep functions a logical, `Default = TRUE` gives intermediate output should be printed. For ML functions a numeric determining if intermediate output should be printed, `Default = 0` does not print, `verbose = 1` prints intermediate output of the parameters and loglikelihood, `verbose = 2` means also intermediate progress during loglikelihood computation is shown.
`trait_pars`	A named list containing diversification rates considering two trait states created by `create_trait_pars`: [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