DAISIE_plot_sims: Plot island species-through-time (STT) plots

In xieshu95/Trait_dependent_TraiSIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Description

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, use_dev_new = TRUE,
  plot_plus_one = TRUE, type = "all_species", Tpars = NULL)

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.
use_dev_new	Boolean to indicate to use dev.new before plotting. Set to TRUE for default behavior. Set to FALSE when plotting within a vignette
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.
type	String to indicate if stt of all species or all possible stt should be plotted. Default is "all_species".
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

Value

R plot.

Author(s)

Luis Valente

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 DAISIE_format_CS

Examples

 

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


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

xieshu95/Trait_dependent_TraiSIE documentation built on Nov. 22, 2019, 7:51 a.m.