In xieshu95/Test-Trasie: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

knitr::opts_chunk$set(
 collapse = TRUE,
 comment = "#>"
)

DAISIE – Dynamic Assembly of Island biotas through Speciation, Immigration and Extinction

Citation: Valente LM, Phillimore AB, Etienne RS (2015) Equilibrium and non- equilibrium dynamics simultaneously operate in the Galápagos islands. Ecology Letters, 18(8), 844-852. https://doi.org/10.1111/ele.12461.

3.2 Data table

To load the package:

library(DAISIE)

3.5 Simulating islands

The function DAISIE_sim allows simulation of DAISIE models and plots the results. The user specifies the parameters to be simulated, the number of replicates, the length of the simulation (typically the island age), and the number of species in the mainland pool.

When the plot_sims option is set to the default (TRUE) the function will produce a species- through-time plot showing the accumulation of total, endemic and non-endemic species through time, as well as confidence intervals for the total number of species.

n_mainland_species <- 1000
island_age <- 2

To shorten the run-time of this vignette, reduce the number of n_replicates. For increased accuracy, increase this number.

n_replicates <- 10

Example 5.1 – Simulating r n_replicates islands with no diversity-dependence, all species sharing the same parameters, and plotting the results

set.seed(42)

clado_rate <- 2.550687345 # cladogenesis rate
ext_rate <- 2.683454548 # extinction rate
clade_carr_cap <- Inf # clade-level carrying capacity
imm_rate <- 0.00933207 # immigration rate
ana_rate <- 1.010073119 # anagenesis rate

island_replicates <- DAISIE_sim( 
  time = island_age,
  M = n_mainland_species, 
  pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
  replicates = n_replicates,
  plot_sims = FALSE,
  verbose = FALSE,
  Apars = NULL
)
DAISIE_plot_sims(island_replicates = island_replicates, use_dev_new = FALSE)

The object island_replicates contains the results of the simulation in DAISIE format. r n_replicates islands are stored in the object, and each island replicate can be viewed separately. For example, type island_replicates[[1]] to view the first replicate.

The element of the list relating to each island contains a table with the number of species through time, as well as branching time information for each independent colonisation event extant at the end of the simulation.

Example 5.2 – Simulating r n_replicates islands with diversity-dependence (K’=10), all species sharing the same parameters, and plotting the results

clado_rate <- 2.550687345 # cladogenesis rate
ext_rate <- 2.683454548 # extinction rate
clade_carr_cap <- 10.0  # clade-level carrying capacity
imm_rate <- 0.00933207 # immigration rate
ana_rate <- 1.010073119 # anagenesis rate

island_replicates_K <- DAISIE_sim( 
  time = island_age, 
  M = n_mainland_species, 
  pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
  replicates = n_replicates,
  plot_sims = FALSE,
  verbose = FALSE
) 
DAISIE_plot_sims(island_replicates_K, use_dev_new = FALSE)

Example 5.3 – Simulating r n_replicates islands allowing Darwin’s finches to have a higher rate of cladogenesis:

clado_rate_1 <- 0.38 # cladogenesis rate
ext_rate_1 <- 0.55 # extinction rate
clade_carr_cap_1 <- Inf  # clade-level carrying capacity
imm_rate_1 <- 0.04 # immigration rate
ana_rate_1 <- 1.10 # anagenesis rate

clado_rate_2 <- 0.38 # cladogenesis rate
ext_rate_2 <- ext_rate_1 # extinction rate
clade_carr_cap_2 <- clade_carr_cap_1  # clade-level carrying capacity
imm_rate_2 <- imm_rate_1 # immigration rate
ana_rate_2 <- ana_rate_1 # anagenesis rate

island_replicates_2types <- DAISIE_sim( 
  time = island_age,
  M = n_mainland_species, 
  pars = c(
    clado_rate_1, ext_rate_1, clade_carr_cap_1, imm_rate_1, ana_rate_1,
    clado_rate_2, ext_rate_2, clade_carr_cap_2, imm_rate_2, ana_rate_2
  ),
  replicates = n_replicates, 
  prop_type2_pool = 0.163,
  plot_sims = TRUE,
  verbose = FALSE
)
DAISIE_plot_sims(island_replicates_2types, use_dev_new = FALSE)

This produces a figure similar to Fig. 2, with three plots: one for the total number of species, one for species of type 1 and one for species of type 2. Accessing each island replicate individually (e.g. island_replicates_2types[[15]]) shows information on branching times and species-through-time tables for total, type 1 species and type 2 species.

xieshu95/Test-Trasie documentation built on Dec. 18, 2019, 7:34 a.m.