DAISIE (version 1.0.2)

DAISIE_format_sim: Converting simulation output from RAW to DAISIE format

Description

Formats islands in RAW format (simulated in DAISIE_sim with format=FALSE) to a DAISIE format

Usage

DAISIE_format_sim(
   island_replicates,
   time,
   M,
   sample_freq
   )

Arguments

island_replicates

Island replicates in RAW format produced in DAISIE_sim with format=FALSE option

time

Length of time the islands were simulated with

M

The size of the mainland pool, i.e the number of species that can potentially colonize the island

sample_freq

Specifies the number of units time should be divided by for plotting purposes. Larger values will lead to plots with higher definition, but will also run slower.

Value

• Each simulated dataset is an element of the list, which can be called using [[x]]. For example if the object is called island_replicates, the 1st replicate can be called using island_replicates[[1]] Each of the island replicates is a list in itself. The first (e.g. island_replicates[[x]][[1]]) element of that list has the following components: $island_age - the island age Then, depending on whether a distinction between types is made, we have: $not_present - the number of mainland lineages that are not present on the island or: $not_present_type1 - the number of mainland lineages of type 1 that are not present on the island $not_present_type2 - the number of mainland lineages of type 2 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 ) $stt_stt_type1 - STT table for type 1 species on the island - only if 2 types of species were simulated (nI - number of non-endemic species; nA - number of anagenetic species, nC - number of cladogenetic species, present - number of independent colonisations present ) $stt_stt_type2 - STT table for type 2 species on the island - only if 2 types of species were simulated (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 4 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) $type_1or2 - whether the colonist belongs to type 1 or type 2

Details

Returns R list object that contains the simulated islands in DAISIE format that can be run on other DAISIE functions.

References

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_plot_sims DAISIE_sim

Examples

data(islands_10reps_RAW)
island_replicates = DAISIE_format_sim(
    island_replicates = islands_10reps_RAW,
    time = 4,
    M = 1000,
    sample_freq = 25
    )