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Plot island species-through-time (STT) plots

Source: R/DAISIE_plot_sims.R
DAISIE_plot_sims.Rd

Produces STT plots. If only one type of species is present in the simulated islands, STT is plotted for all species. If two types are present, three plots are produced: STT for all, STT for type 1 and STT for type 2.

R plots with number of total, endemic and non-endemic STTs for different types of species for the entire time span the islands were simulated. 2.5-97.5th percentiles are plotted in light grey, 25-75th percentiles plotted in dark grey.

Usage

DAISIE_plot_sims(
  island_replicates,
  plot_plus_one = TRUE,
  type = "all_species",
  sample_freq = 25,
  trait_pars = NULL
)

Arguments

island_replicates

List output from DAISIE_sim_core_cr(), DAISIE_sim_core_time_dep(), DAISIE_sim_core_cr_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.

plot_plus_one

Boolean to indicate to plot all values plus one. Set to TRUE for default behavior. Set to FALSE to plot all values without adding one. Only works when there is one type of species.

type

String to indicate if stt of all species or all possible stt should be plotted. Default is "all_species", "type1_species" or "type2_species" should be plotted.

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.

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

Value

R plot.

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_sim_cr, DAISIE_sim_time_dep, DAISIE_sim_cr_shift, DAISIE_format_CS

Author

Luis Valente

Examples



### Plot islands with single process (only one type of species)
utils::data(islands_1type_1000reps)
DAISIE_plot_sims(
  island_replicates = islands_1type_1000reps
  )



### Plot island with type 1 and type 2
utils::data(islands_2types_1000reps)
DAISIE_plot_sims(
  island_replicates = islands_2types_1000reps
  )