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

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

library(DAISIE)

I show TRASIE_CS here:

Here I create params:

n_mainland_species <- 50
island_age <- 4
n_replicates <- 10

clado_rate <- 0.5 # cladogenesis rate
ext_rate <- 0.5 # extinction rate
clade_carr_cap <- 10 # clade-level carrying capacity
imm_rate <- 0.2 # immigration rate
ana_rate <- 1 # anagenesis rate

Tpars_check <- create_trait_state_params(
     trans_rate = 0,
     immig_rate2 = imm_rate,
     ext_rate2 = ext_rate,
     ana_rate2 = ana_rate,
     clado_rate2 = clado_rate,
     trans_rate2 = 0,
     K2 = 10,
     M2 = 50)

Tpars_balance <- create_trait_state_params(
     trans_rate = 0,
     immig_rate2 = imm_rate,
     ext_rate2 = ext_rate,
     ana_rate2 = ana_rate,
     clado_rate2 = clado_rate,
     trans_rate2 = 0,
     K2 = 10,
     M2 = 25)
Tpars_with_trans <- create_trait_state_params(
     trans_rate = 0.1,
     immig_rate2 = imm_rate*0.1,
     ext_rate2 = ext_rate*0.1,
     ana_rate2 = ana_rate*0.1,
     clado_rate2 = clado_rate*0.1,
     trans_rate2 = 0.9,
     K2 = 7,
     M2 = 25)

Here I check TRASIE can create the same simulated rusults as DAISIE using same rate values:

set.seed(42)
DAISIE <- DAISIE_sim( 
  time = island_age,
  M = 50, 
  pars = c(clado_rate, ext_rate, 10, imm_rate, ana_rate),
  replicates = n_replicates,
  Tpars = NULL,    ##  DAISIE only considering one trait states, so Tpars = NULL
  plot_sims = FALSE,
  verbose = FALSE,
  Apars = NULL,
  divdepmodel = "CS"
)

set.seed(42)   ## pars is empty, Tpars use same rate values
TRASIE_check <- DAISIE_sim( 
  time = island_age,
  M = 0, 
  pars = c(0, 0, 0, 0, 0),
  replicates = n_replicates,
  Tpars = Tpars_check,   ## all species on mainland with state 2
  plot_sims = FALSE,
  verbose = FALSE,
  Apars = NULL,
  divdepmodel = "CS"
)

set.seed(42)
TRASIE_balance <- DAISIE_sim( 
  time = island_age,
  M = 25, 
  pars = c(clado_rate, ext_rate, 10, imm_rate, ana_rate),
  replicates = n_replicates,
  Tpars = Tpars_balance,   ## all species on mainland with state 2
  plot_sims = FALSE,
  verbose = FALSE,
  Apars = NULL,
  divdepmodel = "CS"
)

set.seed(42)
TRASIE_with_trans <- DAISIE_sim( 
  time = island_age,
  M = 25, 
  pars = c(clado_rate*1.9, ext_rate*1.9, 3, imm_rate*1.9, ana_rate*1.9),
  replicates = n_replicates,
  Tpars = Tpars_with_trans,   ## all species on mainland with state 2
  plot_sims = FALSE,
  verbose = FALSE,
  Apars = NULL,
  divdepmodel = "CS"
)

Here I show the plots:

DAISIE_plot_sims(island_replicates = DAISIE,Tpars = NULL, use_dev_new = FALSE)

DAISIE_plot_sims(island_replicates = TRASIE_check,Tpars = Tpars_check, use_dev_new = FALSE)

DAISIE_plot_sims(island_replicates = TRASIE_balance,Tpars = Tpars_balance, use_dev_new = FALSE)

DAISIE_plot_sims(island_replicates = TRASIE_with_trans,Tpars = Tpars_with_trans, use_dev_new = FALSE)

For CS model, if diversification rates for two trait states are same, M and M2 will not influence the result when M + M2 is a constant.

Testing the influence of different rates for two states (M = M2)

n_mainland_species <- 25
island_age <- 2
n_replicates <- 100

clado_rate <- 0.5 # cladogenesis rate
ext_rate <- 1 # extinction rate
clade_carr_cap <- 5 # clade-level carrying capacity
imm_rate <- 1 # immigration rate
ana_rate <- 0.5 # anagenesis rate
##  set various level of rate difference between two states
pars1 = c(clado_rate * 0.1, ext_rate * 0.1, clade_carr_cap, imm_rate * 0.1, ana_rate * 0.1)  ## great difference 
pars2 = c(clado_rate * 0.5, ext_rate * 0.5, clade_carr_cap, imm_rate * 0.5, ana_rate * 0.5)  ## median difference
pars3 = c(clado_rate * 0.8, ext_rate * 0.8, clade_carr_cap, imm_rate * 0.8, ana_rate * 0.8)  ## slight difference

Tpars1 <- create_trait_state_params(
     trans_rate = 0,
     immig_rate2 = imm_rate * 1.9,
     ext_rate2 = ext_rate * 1.9,
     ana_rate2 = ana_rate * 1.9,
     clado_rate2 = clado_rate * 1.9,
     trans_rate2 = 0,
     K2 = 5,
     M2 = n_mainland_species)
Tpars2 <- create_trait_state_params(
     trans_rate = 0,
     immig_rate2 = imm_rate * 1.5,
     ext_rate2 = ext_rate * 1.5,
     ana_rate2 = ana_rate * 1.5,
     clado_rate2 = clado_rate * 1.5,
     trans_rate2 = 0,
     K2 = 5,
     M2 = n_mainland_species)
Tpars3 <- create_trait_state_params(
     trans_rate = 0,
     immig_rate2 = imm_rate * 1.2,
     ext_rate2 = ext_rate * 1.2,
     ana_rate2 = ana_rate * 1.2,
     clado_rate2 = clado_rate * 1.2,
     trans_rate2 = 0,
     K2 = 5,
     M2 = n_mainland_species)

set.seed(42)
DAISIE <- DAISIE_sim( 
  time = island_age,
  M = n_mainland_species * 2, 
  pars = pars3,
  replicates = n_replicates,
  Tpars = NULL,
  plot_sims = FALSE,
  verbose = FALSE,
  Apars = NULL,
  divdepmodel = "CS"
)
set.seed(42)
TRASIE1 <- DAISIE_sim( 
  time = island_age,
  M = n_mainland_species, 
  pars = pars1,
  replicates = n_replicates,
  Tpars = Tpars1,
  plot_sims = FALSE,
  verbose = FALSE,
  Apars = NULL,
  divdepmodel = "CS"
)
set.seed(42)
TRASIE2 <- DAISIE_sim( 
  time = island_age,
  M = n_mainland_species, 
  pars = pars2,
  replicates = n_replicates,
  Tpars = Tpars2,
  plot_sims = FALSE,
  verbose = FALSE,
  Apars = NULL,
  divdepmodel = "CS"
)
set.seed(42)
TRASIE3 <- DAISIE_sim( 
  time = island_age,
  M = n_mainland_species, 
  pars = pars3,
  replicates = n_replicates,
  Tpars = Tpars3,
  plot_sims = FALSE,
  verbose = FALSE,
  Apars = NULL,
  divdepmodel = "CS"
)

DAISIE_plot_sims(island_replicates = DAISIE,Tpars = NULL, use_dev_new = FALSE)

DAISIE_plot_sims(island_replicates = TRASIE1,Tpars = Tpars1, use_dev_new = FALSE)

DAISIE_plot_sims(island_replicates = TRASIE2,Tpars = Tpars2, use_dev_new = FALSE)

DAISIE_plot_sims(island_replicates = TRASIE3,Tpars = Tpars3, use_dev_new = FALSE)

compare <- compare_diff(DAISIE_output = DAISIE,
                       TRASIE_output1 = TRASIE1,
                       TRASIE_output2 = TRASIE2,
                       TRASIE_output3 = TRASIE3,
                       Tpars1 = Tpars1,
                       Tpars2 = Tpars2,
                       Tpars3 = Tpars3)

ML_CS_store_params(island_replicates = TRASIE1, pars = pars1)

est_params <- ML_CS_store_params(island_replicates = TRASIE1, pars = pars1)

est_params2 <- ML_CS_store_params(island_replicates = TRASIE2, pars = pars2)
est_params3 <- ML_CS_store_params(island_replicates = TRASIE3, pars = pars3)

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