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 here:
Here I create params:
n_mainland_species <- 1000
island_age <- 4
n_replicates <-10
clado_rate <- 2 # cladogenesis rate
ext_rate <- 2 # extinction rate
island_wide_cap <- 50 # island_wide carrying capacity
imm_rate <- 0.1 # immigration rate
ana_rate <- 1 # anagenesis rate
Tpars_empty <- create_trait_state_params(
trans_rate = 0,
immig_rate2 = 0,
ext_rate2 = 0,
ana_rate2 = 0,
clado_rate2 = 0,
trans_rate2 = 0,
K2 = 0,
M2 = 0)
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 = island_wide_cap,
M2 = n_mainland_species)
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 = island_wide_cap * 0.5,
M2 = n_mainland_species * 0.5)
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 = n_mainland_species,
pars = c(clado_rate, ext_rate, island_wide_cap, 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 = "IW"
)
set.seed(42)
TRASIE_check1 <- DAISIE_sim(
time = island_age,
M = n_mainland_species,
pars = c(clado_rate, ext_rate, island_wide_cap, imm_rate, ana_rate),
replicates = n_replicates,
Tpars = Tpars_empty, ## Tpars is not NULL, but empty
plot_sims = FALSE,
verbose = FALSE,
Apars = NULL,
divdepmodel = "IW"
)
set.seed(42) ## pars is empty, Tpars use same rate values
TRASIE_check2 <- DAISIE_sim(
time = island_age,
M = 0,
pars = c(0, 0, island_wide_cap, 0, 0),
replicates = n_replicates,
Tpars = Tpars_check, ## all species on mainland with state 2
plot_sims = FALSE,
verbose = FALSE,
Apars = NULL,
divdepmodel = "IW"
)
set.seed(42) ## pars is empty, Tpars use same rate values
TRASIE_balance <- DAISIE_sim(
time = island_age,
M = n_mainland_species * 0.5,
pars = c(clado_rate, ext_rate, island_wide_cap * 0.5, 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 = "IW"
)
These are the results:
DAISIE_plot_sims(island_replicates = DAISIE, use_dev_new = FALSE)
DAISIE_plot_sims(island_replicates = TRASIE_check1, Tpars = Tpars_empty, use_dev_new = FALSE)
DAISIE_plot_sims(island_replicates = TRASIE_check2,Tpars = Tpars_check, use_dev_new = FALSE)
DAISIE_plot_sims(island_replicates = TRASIE_balance,Tpars = Tpars_balance, use_dev_new = FALSE)
# compare <- compare_diff2(DAISIE_output = DAISIE,
# TRASIE_output1 = TRASIE_check1,
# TRASIE_output2 = TRASIE_check2,
# TRASIE_output3 = TRASIE_balance,
# Tpars1 = Tpars_empty,
# Tpars2 = Tpars_check,
# Tpars3 = Tpars_balance)
Test the influence of carrying capacity when rates are balance (Mtotal = 1000)
n_mainland_species <- 1000
island_age <- 1
n_replicates <- 50
clado_rate <- 1 # cladogenesis rate
ext_rate <- 1 # extinction rate
island_wide_cap <- 40 # clade-level carrying capacity
imm_rate <- 0.1 # immigration rate
ana_rate <- 0.5 # anagenesis rate
pars = c(clado_rate, ext_rate, island_wide_cap, imm_rate, ana_rate)
pars1 = c(clado_rate*0.5, ext_rate*0.5, 10, imm_rate*0.5, ana_rate*0.5)
pars2 = c(clado_rate*0.5, ext_rate*0.5, 20, imm_rate*0.5, ana_rate*0.5)
pars3 = c(clado_rate*0.5, ext_rate*0.5, 30, imm_rate*0.5, ana_rate*0.5)
Tpars1 <- create_trait_state_params(
trans_rate = 0.3,
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 = 0.1,
K2 = 30,
M2 = 500)
Tpars2 <- create_trait_state_params(
trans_rate = 0.3,
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 = 0.1,
K2 = 20,
M2 = 500)
Tpars3 <- create_trait_state_params(
trans_rate = 0.3,
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 = 0.1,
K2 = 10,
M2 = 500)
set.seed(42)
DAISIE <- DAISIE_sim(
time = island_age,
M = n_mainland_species,
pars = pars,
replicates = n_replicates,
Tpars = NULL,
plot_sims = FALSE,
verbose = FALSE,
Apars = NULL,
divdepmodel = "IW",
sample_freq = 50
)
set.seed(42)
TRASIE1 <- DAISIE_sim(
time = island_age,
M = 500,
pars = pars1,
replicates = n_replicates,
Tpars = Tpars1,
plot_sims = FALSE,
verbose = FALSE,
Apars = NULL,
divdepmodel = "IW",
sample_freq = 50
)
set.seed(42)
TRASIE2 <- DAISIE_sim(
time = island_age,
M = 500,
pars = pars2,
replicates = n_replicates,
Tpars = Tpars2,
plot_sims = FALSE,
verbose = FALSE,
Apars = NULL,
divdepmodel = "IW",
sample_freq = 50
)
set.seed(42)
TRASIE3 <- DAISIE_sim(
time = island_age,
M = 500,
pars = pars3,
replicates = n_replicates,
Tpars = Tpars3,
plot_sims = FALSE,
verbose = FALSE,
Apars = NULL,
divdepmodel = "IW",
sample_freq = 50
)
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)
Test the influence of M when rates are balance (Mtotal = 1000)
n_mainland_species <- 1000
island_age <- 4
n_replicates <- 30
clado_rate <- 2 # cladogenesis rate
ext_rate <- 2 # extinction rate
island_wide_cap <- 10 # clade-level carrying capacity
imm_rate <- 0.01 # immigration rate
ana_rate <- 1 # anagenesis rate
pars = c(clado_rate, ext_rate, island_wide_cap, imm_rate, ana_rate)
Tpars1 <- 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 = 100)
Tpars2 <- 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 = 250)
Tpars3 <- 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 = 500)
# Tpars4 <- 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,
# M2 = 750)
set.seed(42)
DAISIE <- DAISIE_sim(
time = island_age,
M = n_mainland_species,
pars = pars,
replicates = n_replicates,
Tpars = NULL,
plot_sims = FALSE,
verbose = FALSE,
Apars = NULL,
divdepmodel = "IW",
sample_freq = 50
)
set.seed(42)
TRASIE1 <- DAISIE_sim(
time = island_age,
M = 900,
pars = pars,
replicates = n_replicates,
Tpars = Tpars1,
plot_sims = FALSE,
verbose = FALSE,
Apars = NULL,
divdepmodel = "IW",
sample_freq = 50
)
set.seed(42)
TRASIE2 <- DAISIE_sim(
time = island_age,
M = 750,
pars = pars,
replicates = n_replicates,
Tpars = Tpars2,
plot_sims = FALSE,
verbose = FALSE,
Apars = NULL,
divdepmodel = "IW",
sample_freq = 50
)
set.seed(42)
TRASIE3 <- DAISIE_sim(
time = island_age,
M = 500,
pars = pars,
replicates = n_replicates,
Tpars = Tpars3,
plot_sims = FALSE,
verbose = FALSE,
Apars = NULL,
divdepmodel = "IW",
sample_freq = 50
)
# set.seed(42)
# TRASIE4 <- DAISIE_sim(
# time = island_age,
# M = 250,
# pars = pars,
# replicates = n_replicates,
# Tpars = Tpars4,
# plot_sims = FALSE,
# verbose = FALSE,
# Apars = NULL,
# divdepmodel = "IW",
# sample_freq = 50
# )
compare <- compare_diff(DAISIE_output = DAISIE,
TRASIE_output1 = TRASIE1,
TRASIE_output2 = TRASIE2,
TRASIE_output3 = TRASIE3,
Tpars1 = Tpars1,
Tpars2 = Tpars2,
Tpars3 = Tpars3)
Testing the influence of rates deviation between two trait states when M = M2
n_mainland_species <- 500
island_age <- 4
n_replicates <- 100
clado_rate <- 2 # cladogenesis rate
ext_rate <- 2 # extinction rate
island_wide_cap <- 10 # clade-level carrying capacity
imm_rate <- 0.01 # immigration rate
ana_rate <- 1 # anagenesis rate
## set various level of rate difference between two states
pars1 = c(clado_rate * 0.1, ext_rate * 0.1, island_wide_cap, imm_rate * 0.1, ana_rate * 0.1) ## great difference
pars2 = c(clado_rate * 0.8, ext_rate * 0.8, island_wide_cap, imm_rate * 0.8, ana_rate * 0.8) ## slight difference
pars3 = c(clado_rate, ext_rate, island_wide_cap, imm_rate, ana_rate) ## same rates
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 = 10,
M2 = n_mainland_species
)
Tpars2 <- 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 = 10,
M2 = n_mainland_species)
Tpars3 <- 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 = 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 = "IW"
# sample_freq = 50
)
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 = "IW"
# sample_freq = 50
)
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 = "IW"
# sample_freq = 50
)
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 = "IW"
# sample_freq = 50
)
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)
Testing the influence of transition rate. Here I show the results using different rates for two trait states(set same number of species on mainland with different states M = M2), and compare them with the result from DAISIE using average rates of two states:
n_mainland_species <- 500
island_age <- 4
n_replicates <- 30
clado_rate <- 2 # cladogenesis rate
ext_rate <- 2 # extinction rate
island_wide_cap <- 10 # clade-level carrying capacity
imm_rate <- 0.01 # immigration rate
ana_rate <- 1 # anagenesis rate
pars_ave = c(clado_rate, ext_rate, island_wide_cap, imm_rate, ana_rate)
pars1 = c(clado_rate * 0.1, ext_rate * 0.1, island_wide_cap, imm_rate * 0.1, ana_rate * 0.1)
Tpars1_notrans <- 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 = 10,
M2 = n_mainland_species)
Tpars1_trans1 <- create_trait_state_params(
trans_rate = 0.5,
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 = 0.5,
K2 = 10,
M2 = n_mainland_species)
Tpars1_trans2 <- create_trait_state_params(
trans_rate = 0.1,
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 = 0.9,
K2 = 10,
M2 = n_mainland_species)
# Tpars1_trans3 <- create_trait_state_params(
# trans_rate = 0.9,
# 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 = 0.1,
# M2 = n_mainland_species)
set.seed(42)
DAISIE_ave <- DAISIE_sim(
time = island_age,
M = n_mainland_species * 2,
pars = pars_ave,
replicates = n_replicates,
Tpars = NULL,
plot_sims = FALSE,
verbose = FALSE,
Apars = NULL,
divdepmodel = "IW",
sample_freq = 50
)
set.seed(42)
TRASIE1_notrans <- DAISIE_sim(
time = island_age,
M = n_mainland_species,
pars = pars1,
replicates = n_replicates,
Tpars = Tpars1_notrans,
plot_sims = FALSE,
verbose = FALSE,
Apars = NULL,
divdepmodel = "IW",
sample_freq = 50
)
set.seed(42)
TRASIE1_trans1 <- DAISIE_sim(
time = island_age,
M = n_mainland_species,
pars = pars1,
replicates = n_replicates,
Tpars = Tpars1_trans1,
plot_sims = FALSE,
verbose = FALSE,
Apars = NULL,
divdepmodel = "IW",
sample_freq = 50
)
set.seed(42)
TRASIE1_trans2 <- DAISIE_sim(
time = island_age,
M = n_mainland_species,
pars = pars1,
replicates = n_replicates,
Tpars = Tpars1_trans2,
plot_sims = FALSE,
verbose = FALSE,
Apars = NULL,
divdepmodel = "IW",
sample_freq = 50
)
# set.seed(42)
# TRASIE1_trans3 <- DAISIE_sim(
# time = island_age,
# M = n_mainland_species,
# pars = pars1,
# replicates = n_replicates,
# Tpars = Tpars1_trans3,
# plot_sims = FALSE,
# verbose = FALSE,
# Apars = NULL,
# divdepmodel = "IW"
# )
Here I show the plots:
DAISIE_plot_sims(island_replicates = DAISIE_ave,Tpars = NULL, use_dev_new = FALSE)
DAISIE_plot_sims(island_replicates = TRASIE1_notrans,Tpars = Tpars1_notrans, use_dev_new = FALSE)
DAISIE_plot_sims(island_replicates = TRASIE1_trans1,Tpars = Tpars1_trans1, use_dev_new = FALSE)
DAISIE_plot_sims(island_replicates = TRASIE1_trans2,Tpars = Tpars1_trans2, use_dev_new = FALSE)
Comparing average
compare <- compare_diff(DAISIE_output = DAISIE_ave,
TRASIE_output1 = TRASIE1_notrans,
TRASIE_output2 = TRASIE1_trans1,
TRASIE_output3 = TRASIE1_trans2,
Tpars1 = Tpars1_notrans,
Tpars2 = Tpars1_trans1,
Tpars3 = Tpars1_trans2)
Testing simulated results when everything is unbalance
n_mainland_species <- 1000
island_age <- 2
n_replicates <- 30
clado_rate <- 2 # cladogenesis rate
ext_rate <- 2 # extinction rate
island_wide_cap <- 20 # clade-level carrying capacity
imm_rate <- 0.1 # immigration rate
ana_rate <- 1 # anagenesis rate
## set various level of rate difference between two states
pars1 = c(clado_rate * 0.1, ext_rate * 0.1, island_wide_cap, imm_rate * 0.1, ana_rate * 0.1)
pars_ave = c(clado_rate * 0.5, ext_rate * 0.5, island_wide_cap, imm_rate * 0.5, ana_rate * 0.5) ## DAISIE_ave
Tpars1 <- create_trait_state_params(
trans_rate = 0.5,
immig_rate2 = imm_rate * 0.9,
ext_rate2 = ext_rate * 0.9,
ana_rate2 = ana_rate * 0.9,
clado_rate2 = clado_rate * 0.9,
trans_rate2 = 0.5,
K2 = island_wide_cap * 0.9,
M2 = n_mainland_species * 0.9
)
Tpars2 <- create_trait_state_params(
trans_rate = 0.5,
immig_rate2 = imm_rate * 0.9,
ext_rate2 = ext_rate * 0.9,
ana_rate2 = ana_rate * 0.9,
clado_rate2 = clado_rate * 0.9,
trans_rate2 = 0.5,
K2 = island_wide_cap * 0.9,
M2 = n_mainland_species * 0.1)
Tpars3 <- create_trait_state_params(
trans_rate = 0.9,
immig_rate2 = imm_rate * 0.9,
ext_rate2 = ext_rate * 0.9,
ana_rate2 = ana_rate * 0.9,
clado_rate2 = clado_rate * 0.9,
trans_rate2 = 0.1,
K2 = island_wide_cap * 0.9,
M2 = n_mainland_species * 0.9
)
set.seed(42)
DAISIE<- DAISIE_sim(
time = island_age,
M = n_mainland_species,
pars = pars_ave,
replicates = n_replicates,
Tpars = NULL,
plot_sims = FALSE,
verbose = FALSE,
Apars = NULL,
divdepmodel = "IW",
sample_freq = 50
)
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 = "IW",
sample_freq = 50
)
set.seed(42)
TRASIE2 <- DAISIE_sim(
time = island_age,
M = n_mainland_species,
pars = pars1,
replicates = n_replicates,
Tpars = Tpars2,
plot_sims = FALSE,
verbose = FALSE,
Apars = NULL,
divdepmodel = "IW",
sample_freq = 50
)
set.seed(42)
TRASIE3<- DAISIE_sim(
time = island_age,
M = n_mainland_species,
pars = pars1,
replicates = n_replicates,
Tpars = Tpars3,
plot_sims = FALSE,
verbose = FALSE,
Apars = NULL,
divdepmodel = "IW",
sample_freq = 50
)
compare <- compare_diff(DAISIE_output = DAISIE,
TRASIE_output1 = TRASIE1,
TRASIE_output2 = TRASIE2,
TRASIE_output3 = TRASIE3,
Tpars1 = Tpars1,
Tpars2 = Tpars2,
Tpars3 = Tpars3)
xieshu95/Trait_dependent_TraiSIE documentation built on Nov. 22, 2019, 7:51 a.m.
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knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
library(DAISIE)
I show TRASIE here:
Here I create params:
n_mainland_species <- 1000 island_age <- 4 n_replicates <-10 clado_rate <- 2 # cladogenesis rate ext_rate <- 2 # extinction rate island_wide_cap <- 50 # island_wide carrying capacity imm_rate <- 0.1 # immigration rate ana_rate <- 1 # anagenesis rate Tpars_empty <- create_trait_state_params( trans_rate = 0, immig_rate2 = 0, ext_rate2 = 0, ana_rate2 = 0, clado_rate2 = 0, trans_rate2 = 0, K2 = 0, M2 = 0) 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 = island_wide_cap, M2 = n_mainland_species) 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 = island_wide_cap * 0.5, M2 = n_mainland_species * 0.5)
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 = n_mainland_species, pars = c(clado_rate, ext_rate, island_wide_cap, 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 = "IW" ) set.seed(42) TRASIE_check1 <- DAISIE_sim( time = island_age, M = n_mainland_species, pars = c(clado_rate, ext_rate, island_wide_cap, imm_rate, ana_rate), replicates = n_replicates, Tpars = Tpars_empty, ## Tpars is not NULL, but empty plot_sims = FALSE, verbose = FALSE, Apars = NULL, divdepmodel = "IW" ) set.seed(42) ## pars is empty, Tpars use same rate values TRASIE_check2 <- DAISIE_sim( time = island_age, M = 0, pars = c(0, 0, island_wide_cap, 0, 0), replicates = n_replicates, Tpars = Tpars_check, ## all species on mainland with state 2 plot_sims = FALSE, verbose = FALSE, Apars = NULL, divdepmodel = "IW" ) set.seed(42) ## pars is empty, Tpars use same rate values TRASIE_balance <- DAISIE_sim( time = island_age, M = n_mainland_species * 0.5, pars = c(clado_rate, ext_rate, island_wide_cap * 0.5, 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 = "IW" )
These are the results:
DAISIE_plot_sims(island_replicates = DAISIE, use_dev_new = FALSE)
DAISIE_plot_sims(island_replicates = TRASIE_check1, Tpars = Tpars_empty, use_dev_new = FALSE)
DAISIE_plot_sims(island_replicates = TRASIE_check2,Tpars = Tpars_check, use_dev_new = FALSE)
DAISIE_plot_sims(island_replicates = TRASIE_balance,Tpars = Tpars_balance, use_dev_new = FALSE)
# compare <- compare_diff2(DAISIE_output = DAISIE, # TRASIE_output1 = TRASIE_check1, # TRASIE_output2 = TRASIE_check2, # TRASIE_output3 = TRASIE_balance, # Tpars1 = Tpars_empty, # Tpars2 = Tpars_check, # Tpars3 = Tpars_balance)
Test the influence of carrying capacity when rates are balance (Mtotal = 1000)
n_mainland_species <- 1000 island_age <- 1 n_replicates <- 50 clado_rate <- 1 # cladogenesis rate ext_rate <- 1 # extinction rate island_wide_cap <- 40 # clade-level carrying capacity imm_rate <- 0.1 # immigration rate ana_rate <- 0.5 # anagenesis rate pars = c(clado_rate, ext_rate, island_wide_cap, imm_rate, ana_rate) pars1 = c(clado_rate*0.5, ext_rate*0.5, 10, imm_rate*0.5, ana_rate*0.5) pars2 = c(clado_rate*0.5, ext_rate*0.5, 20, imm_rate*0.5, ana_rate*0.5) pars3 = c(clado_rate*0.5, ext_rate*0.5, 30, imm_rate*0.5, ana_rate*0.5) Tpars1 <- create_trait_state_params( trans_rate = 0.3, 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 = 0.1, K2 = 30, M2 = 500) Tpars2 <- create_trait_state_params( trans_rate = 0.3, 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 = 0.1, K2 = 20, M2 = 500) Tpars3 <- create_trait_state_params( trans_rate = 0.3, 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 = 0.1, K2 = 10, M2 = 500)
set.seed(42) DAISIE <- DAISIE_sim( time = island_age, M = n_mainland_species, pars = pars, replicates = n_replicates, Tpars = NULL, plot_sims = FALSE, verbose = FALSE, Apars = NULL, divdepmodel = "IW", sample_freq = 50 ) set.seed(42) TRASIE1 <- DAISIE_sim( time = island_age, M = 500, pars = pars1, replicates = n_replicates, Tpars = Tpars1, plot_sims = FALSE, verbose = FALSE, Apars = NULL, divdepmodel = "IW", sample_freq = 50 ) set.seed(42) TRASIE2 <- DAISIE_sim( time = island_age, M = 500, pars = pars2, replicates = n_replicates, Tpars = Tpars2, plot_sims = FALSE, verbose = FALSE, Apars = NULL, divdepmodel = "IW", sample_freq = 50 ) set.seed(42) TRASIE3 <- DAISIE_sim( time = island_age, M = 500, pars = pars3, replicates = n_replicates, Tpars = Tpars3, plot_sims = FALSE, verbose = FALSE, Apars = NULL, divdepmodel = "IW", sample_freq = 50 )
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)
Test the influence of M when rates are balance (Mtotal = 1000)
n_mainland_species <- 1000 island_age <- 4 n_replicates <- 30 clado_rate <- 2 # cladogenesis rate ext_rate <- 2 # extinction rate island_wide_cap <- 10 # clade-level carrying capacity imm_rate <- 0.01 # immigration rate ana_rate <- 1 # anagenesis rate pars = c(clado_rate, ext_rate, island_wide_cap, imm_rate, ana_rate) Tpars1 <- 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 = 100) Tpars2 <- 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 = 250) Tpars3 <- 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 = 500) # Tpars4 <- 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, # M2 = 750) set.seed(42) DAISIE <- DAISIE_sim( time = island_age, M = n_mainland_species, pars = pars, replicates = n_replicates, Tpars = NULL, plot_sims = FALSE, verbose = FALSE, Apars = NULL, divdepmodel = "IW", sample_freq = 50 ) set.seed(42) TRASIE1 <- DAISIE_sim( time = island_age, M = 900, pars = pars, replicates = n_replicates, Tpars = Tpars1, plot_sims = FALSE, verbose = FALSE, Apars = NULL, divdepmodel = "IW", sample_freq = 50 ) set.seed(42) TRASIE2 <- DAISIE_sim( time = island_age, M = 750, pars = pars, replicates = n_replicates, Tpars = Tpars2, plot_sims = FALSE, verbose = FALSE, Apars = NULL, divdepmodel = "IW", sample_freq = 50 ) set.seed(42) TRASIE3 <- DAISIE_sim( time = island_age, M = 500, pars = pars, replicates = n_replicates, Tpars = Tpars3, plot_sims = FALSE, verbose = FALSE, Apars = NULL, divdepmodel = "IW", sample_freq = 50 ) # set.seed(42) # TRASIE4 <- DAISIE_sim( # time = island_age, # M = 250, # pars = pars, # replicates = n_replicates, # Tpars = Tpars4, # plot_sims = FALSE, # verbose = FALSE, # Apars = NULL, # divdepmodel = "IW", # sample_freq = 50 # )
compare <- compare_diff(DAISIE_output = DAISIE, TRASIE_output1 = TRASIE1, TRASIE_output2 = TRASIE2, TRASIE_output3 = TRASIE3, Tpars1 = Tpars1, Tpars2 = Tpars2, Tpars3 = Tpars3)
Testing the influence of rates deviation between two trait states when M = M2
n_mainland_species <- 500 island_age <- 4 n_replicates <- 100 clado_rate <- 2 # cladogenesis rate ext_rate <- 2 # extinction rate island_wide_cap <- 10 # clade-level carrying capacity imm_rate <- 0.01 # immigration rate ana_rate <- 1 # anagenesis rate ## set various level of rate difference between two states pars1 = c(clado_rate * 0.1, ext_rate * 0.1, island_wide_cap, imm_rate * 0.1, ana_rate * 0.1) ## great difference pars2 = c(clado_rate * 0.8, ext_rate * 0.8, island_wide_cap, imm_rate * 0.8, ana_rate * 0.8) ## slight difference pars3 = c(clado_rate, ext_rate, island_wide_cap, imm_rate, ana_rate) ## same rates 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 = 10, M2 = n_mainland_species ) Tpars2 <- 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 = 10, M2 = n_mainland_species) Tpars3 <- 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 = 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 = "IW" # sample_freq = 50 ) 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 = "IW" # sample_freq = 50 ) 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 = "IW" # sample_freq = 50 ) 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 = "IW" # sample_freq = 50 )
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)
Testing the influence of transition rate. Here I show the results using different rates for two trait states(set same number of species on mainland with different states M = M2), and compare them with the result from DAISIE using average rates of two states:
n_mainland_species <- 500 island_age <- 4 n_replicates <- 30 clado_rate <- 2 # cladogenesis rate ext_rate <- 2 # extinction rate island_wide_cap <- 10 # clade-level carrying capacity imm_rate <- 0.01 # immigration rate ana_rate <- 1 # anagenesis rate pars_ave = c(clado_rate, ext_rate, island_wide_cap, imm_rate, ana_rate) pars1 = c(clado_rate * 0.1, ext_rate * 0.1, island_wide_cap, imm_rate * 0.1, ana_rate * 0.1) Tpars1_notrans <- 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 = 10, M2 = n_mainland_species) Tpars1_trans1 <- create_trait_state_params( trans_rate = 0.5, 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 = 0.5, K2 = 10, M2 = n_mainland_species) Tpars1_trans2 <- create_trait_state_params( trans_rate = 0.1, 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 = 0.9, K2 = 10, M2 = n_mainland_species) # Tpars1_trans3 <- create_trait_state_params( # trans_rate = 0.9, # 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 = 0.1, # M2 = n_mainland_species) set.seed(42) DAISIE_ave <- DAISIE_sim( time = island_age, M = n_mainland_species * 2, pars = pars_ave, replicates = n_replicates, Tpars = NULL, plot_sims = FALSE, verbose = FALSE, Apars = NULL, divdepmodel = "IW", sample_freq = 50 ) set.seed(42) TRASIE1_notrans <- DAISIE_sim( time = island_age, M = n_mainland_species, pars = pars1, replicates = n_replicates, Tpars = Tpars1_notrans, plot_sims = FALSE, verbose = FALSE, Apars = NULL, divdepmodel = "IW", sample_freq = 50 ) set.seed(42) TRASIE1_trans1 <- DAISIE_sim( time = island_age, M = n_mainland_species, pars = pars1, replicates = n_replicates, Tpars = Tpars1_trans1, plot_sims = FALSE, verbose = FALSE, Apars = NULL, divdepmodel = "IW", sample_freq = 50 ) set.seed(42) TRASIE1_trans2 <- DAISIE_sim( time = island_age, M = n_mainland_species, pars = pars1, replicates = n_replicates, Tpars = Tpars1_trans2, plot_sims = FALSE, verbose = FALSE, Apars = NULL, divdepmodel = "IW", sample_freq = 50 ) # set.seed(42) # TRASIE1_trans3 <- DAISIE_sim( # time = island_age, # M = n_mainland_species, # pars = pars1, # replicates = n_replicates, # Tpars = Tpars1_trans3, # plot_sims = FALSE, # verbose = FALSE, # Apars = NULL, # divdepmodel = "IW" # )
Here I show the plots:
DAISIE_plot_sims(island_replicates = DAISIE_ave,Tpars = NULL, use_dev_new = FALSE)
DAISIE_plot_sims(island_replicates = TRASIE1_notrans,Tpars = Tpars1_notrans, use_dev_new = FALSE)
DAISIE_plot_sims(island_replicates = TRASIE1_trans1,Tpars = Tpars1_trans1, use_dev_new = FALSE)
DAISIE_plot_sims(island_replicates = TRASIE1_trans2,Tpars = Tpars1_trans2, use_dev_new = FALSE)
Comparing average
compare <- compare_diff(DAISIE_output = DAISIE_ave, TRASIE_output1 = TRASIE1_notrans, TRASIE_output2 = TRASIE1_trans1, TRASIE_output3 = TRASIE1_trans2, Tpars1 = Tpars1_notrans, Tpars2 = Tpars1_trans1, Tpars3 = Tpars1_trans2)
Testing simulated results when everything is unbalance
n_mainland_species <- 1000 island_age <- 2 n_replicates <- 30 clado_rate <- 2 # cladogenesis rate ext_rate <- 2 # extinction rate island_wide_cap <- 20 # clade-level carrying capacity imm_rate <- 0.1 # immigration rate ana_rate <- 1 # anagenesis rate ## set various level of rate difference between two states pars1 = c(clado_rate * 0.1, ext_rate * 0.1, island_wide_cap, imm_rate * 0.1, ana_rate * 0.1) pars_ave = c(clado_rate * 0.5, ext_rate * 0.5, island_wide_cap, imm_rate * 0.5, ana_rate * 0.5) ## DAISIE_ave Tpars1 <- create_trait_state_params( trans_rate = 0.5, immig_rate2 = imm_rate * 0.9, ext_rate2 = ext_rate * 0.9, ana_rate2 = ana_rate * 0.9, clado_rate2 = clado_rate * 0.9, trans_rate2 = 0.5, K2 = island_wide_cap * 0.9, M2 = n_mainland_species * 0.9 ) Tpars2 <- create_trait_state_params( trans_rate = 0.5, immig_rate2 = imm_rate * 0.9, ext_rate2 = ext_rate * 0.9, ana_rate2 = ana_rate * 0.9, clado_rate2 = clado_rate * 0.9, trans_rate2 = 0.5, K2 = island_wide_cap * 0.9, M2 = n_mainland_species * 0.1) Tpars3 <- create_trait_state_params( trans_rate = 0.9, immig_rate2 = imm_rate * 0.9, ext_rate2 = ext_rate * 0.9, ana_rate2 = ana_rate * 0.9, clado_rate2 = clado_rate * 0.9, trans_rate2 = 0.1, K2 = island_wide_cap * 0.9, M2 = n_mainland_species * 0.9 ) set.seed(42) DAISIE<- DAISIE_sim( time = island_age, M = n_mainland_species, pars = pars_ave, replicates = n_replicates, Tpars = NULL, plot_sims = FALSE, verbose = FALSE, Apars = NULL, divdepmodel = "IW", sample_freq = 50 ) 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 = "IW", sample_freq = 50 ) set.seed(42) TRASIE2 <- DAISIE_sim( time = island_age, M = n_mainland_species, pars = pars1, replicates = n_replicates, Tpars = Tpars2, plot_sims = FALSE, verbose = FALSE, Apars = NULL, divdepmodel = "IW", sample_freq = 50 ) set.seed(42) TRASIE3<- DAISIE_sim( time = island_age, M = n_mainland_species, pars = pars1, replicates = n_replicates, Tpars = Tpars3, plot_sims = FALSE, verbose = FALSE, Apars = NULL, divdepmodel = "IW", sample_freq = 50 )
compare <- compare_diff(DAISIE_output = DAISIE, TRASIE_output1 = TRASIE1, TRASIE_output2 = TRASIE2, TRASIE_output3 = TRASIE3, Tpars1 = Tpars1, Tpars2 = Tpars2, Tpars3 = Tpars3)
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