In xieshu95/Trait_dependent_TraiSIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
library(DAISIE)
Here I create params:
n_mainland_species <- 500
island_age <- 4
n_replicates <- 50
clado_rate <- 2 # cladogenesis rate
ext_rate <- 2 # extinction rate
island_wide_cap <- 20 # 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, ext_rate, island_wide_cap, imm_rate * 0.1, ana_rate) ## great difference
pars2 = c(clado_rate, ext_rate, island_wide_cap, imm_rate * 0.8, ana_rate) ## 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,
ana_rate2 = ana_rate,
clado_rate2 = clado_rate,
trans_rate2 = 0,
M2 = n_mainland_species
)
Tpars2 <- create_trait_state_params(
trans_rate = 0,
immig_rate2 = imm_rate * 1.2,
ext_rate2 = ext_rate,
ana_rate2 = ana_rate,
clado_rate2 = clado_rate,
trans_rate2 = 0,
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,
M2 = n_mainland_species)
Here I test if using different immigration rates for two trait states will influence sinmulation results
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)
compare = compare_diff2(DAISIE_output = DAISIE,
TRASIE_output1 = TRASIE1,
TRASIE_output2 = TRASIE2,
TRASIE_output3 = TRASIE3,
Tpars1 = Tpars1,
Tpars2 = Tpars2,
Tpars3 = Tpars3)
n_mainland_species <- 500
island_age <- 4
n_replicates <- 50
clado_rate <- 2 # cladogenesis rate
ext_rate <- 2 # extinction rate
island_wide_cap <- 20 # clade-level carrying capacity
imm_rate <- 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, island_wide_cap, imm_rate, ana_rate) ## great difference
pars2 = c(clado_rate * 0.4, ext_rate, island_wide_cap, imm_rate, ana_rate) ## slight difference
pars3 = c(clado_rate * 0.5, ext_rate, island_wide_cap, imm_rate, ana_rate) ## same rates
Tpars1 <- create_trait_state_params(
trans_rate = 0,
immig_rate2 = imm_rate,
ext_rate2 = ext_rate,
ana_rate2 = ana_rate,
clado_rate2 = clado_rate * 0.9,
trans_rate2 = 0,
M2 = n_mainland_species
)
Tpars2 <- create_trait_state_params(
trans_rate = 0,
immig_rate2 = imm_rate,
ext_rate2 = ext_rate,
ana_rate2 = ana_rate,
clado_rate2 = clado_rate * 0.6,
trans_rate2 = 0,
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 * 0.5,
trans_rate2 = 0,
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 = 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)
compare = compare_diff2(DAISIE_output = DAISIE,
TRASIE_output1 = TRASIE1,
TRASIE_output2 = TRASIE2,
TRASIE_output3 = TRASIE3,
Tpars1 = Tpars1,
Tpars2 = Tpars2,
Tpars3 = Tpars3)
Here test the influence of unbalance extinction rate
n_mainland_species <- 500
island_age <- 4
n_replicates <- 50
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, ext_rate * 0.1, island_wide_cap, imm_rate, ana_rate) ## great difference
pars2 = c(clado_rate, ext_rate * 0.4, island_wide_cap, imm_rate, ana_rate) ## slight difference
pars3 = c(clado_rate, ext_rate * 0.5, island_wide_cap, imm_rate, ana_rate) ## same rates
Tpars1 <- create_trait_state_params(
trans_rate = 0,
immig_rate2 = imm_rate,
ext_rate2 = ext_rate * 0.9,
ana_rate2 = ana_rate,
clado_rate2 = clado_rate,
trans_rate2 = 0,
M2 = n_mainland_species
)
Tpars2 <- create_trait_state_params(
trans_rate = 0,
immig_rate2 = imm_rate,
ext_rate2 = ext_rate * 0.6,
ana_rate2 = ana_rate,
clado_rate2 = clado_rate,
trans_rate2 = 0,
M2 = n_mainland_species)
Tpars3 <- create_trait_state_params(
trans_rate = 0,
immig_rate2 = imm_rate,
ext_rate2 = ext_rate * 0.5,
ana_rate2 = ana_rate,
clado_rate2 = clado_rate,
trans_rate2 = 0,
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 = 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)
compare = compare_diff2(DAISIE_output = DAISIE,
TRASIE_output1 = TRASIE1,
TRASIE_output2 = TRASIE2,
TRASIE_output3 = TRASIE3,
Tpars1 = Tpars1,
Tpars2 = Tpars2,
Tpars3 = Tpars3)
n_mainland_species <- 500
island_age <- 4
n_replicates <- 50
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, ext_rate * 0.1, island_wide_cap, imm_rate, ana_rate) ## great difference
pars2 = c(clado_rate, ext_rate * 0.8, island_wide_cap, imm_rate, ana_rate) ## 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,
ext_rate2 = ext_rate * 1.9,
ana_rate2 = ana_rate,
clado_rate2 = clado_rate,
trans_rate2 = 0,
M2 = n_mainland_species
)
Tpars2 <- create_trait_state_params(
trans_rate = 0,
immig_rate2 = imm_rate,
ext_rate2 = ext_rate * 1.2,
ana_rate2 = ana_rate,
clado_rate2 = clado_rate,
trans_rate2 = 0,
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,
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 = TRASIE3,Tpars = Tpars3, use_dev_new = FALSE)
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)
Here I create params:
n_mainland_species <- 500 island_age <- 4 n_replicates <- 50 clado_rate <- 2 # cladogenesis rate ext_rate <- 2 # extinction rate island_wide_cap <- 20 # 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, ext_rate, island_wide_cap, imm_rate * 0.1, ana_rate) ## great difference pars2 = c(clado_rate, ext_rate, island_wide_cap, imm_rate * 0.8, ana_rate) ## 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, ana_rate2 = ana_rate, clado_rate2 = clado_rate, trans_rate2 = 0, M2 = n_mainland_species ) Tpars2 <- create_trait_state_params( trans_rate = 0, immig_rate2 = imm_rate * 1.2, ext_rate2 = ext_rate, ana_rate2 = ana_rate, clado_rate2 = clado_rate, trans_rate2 = 0, 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, M2 = n_mainland_species)
Here I test if using different immigration rates for two trait states will influence sinmulation results
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)
compare = compare_diff2(DAISIE_output = DAISIE, TRASIE_output1 = TRASIE1, TRASIE_output2 = TRASIE2, TRASIE_output3 = TRASIE3, Tpars1 = Tpars1, Tpars2 = Tpars2, Tpars3 = Tpars3)
n_mainland_species <- 500 island_age <- 4 n_replicates <- 50 clado_rate <- 2 # cladogenesis rate ext_rate <- 2 # extinction rate island_wide_cap <- 20 # clade-level carrying capacity imm_rate <- 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, island_wide_cap, imm_rate, ana_rate) ## great difference pars2 = c(clado_rate * 0.4, ext_rate, island_wide_cap, imm_rate, ana_rate) ## slight difference pars3 = c(clado_rate * 0.5, ext_rate, island_wide_cap, imm_rate, ana_rate) ## same rates Tpars1 <- create_trait_state_params( trans_rate = 0, immig_rate2 = imm_rate, ext_rate2 = ext_rate, ana_rate2 = ana_rate, clado_rate2 = clado_rate * 0.9, trans_rate2 = 0, M2 = n_mainland_species ) Tpars2 <- create_trait_state_params( trans_rate = 0, immig_rate2 = imm_rate, ext_rate2 = ext_rate, ana_rate2 = ana_rate, clado_rate2 = clado_rate * 0.6, trans_rate2 = 0, 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 * 0.5, trans_rate2 = 0, 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 = 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)
compare = compare_diff2(DAISIE_output = DAISIE, TRASIE_output1 = TRASIE1, TRASIE_output2 = TRASIE2, TRASIE_output3 = TRASIE3, Tpars1 = Tpars1, Tpars2 = Tpars2, Tpars3 = Tpars3)
Here test the influence of unbalance extinction rate
n_mainland_species <- 500 island_age <- 4 n_replicates <- 50 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, ext_rate * 0.1, island_wide_cap, imm_rate, ana_rate) ## great difference pars2 = c(clado_rate, ext_rate * 0.4, island_wide_cap, imm_rate, ana_rate) ## slight difference pars3 = c(clado_rate, ext_rate * 0.5, island_wide_cap, imm_rate, ana_rate) ## same rates Tpars1 <- create_trait_state_params( trans_rate = 0, immig_rate2 = imm_rate, ext_rate2 = ext_rate * 0.9, ana_rate2 = ana_rate, clado_rate2 = clado_rate, trans_rate2 = 0, M2 = n_mainland_species ) Tpars2 <- create_trait_state_params( trans_rate = 0, immig_rate2 = imm_rate, ext_rate2 = ext_rate * 0.6, ana_rate2 = ana_rate, clado_rate2 = clado_rate, trans_rate2 = 0, M2 = n_mainland_species) Tpars3 <- create_trait_state_params( trans_rate = 0, immig_rate2 = imm_rate, ext_rate2 = ext_rate * 0.5, ana_rate2 = ana_rate, clado_rate2 = clado_rate, trans_rate2 = 0, 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 = 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)
compare = compare_diff2(DAISIE_output = DAISIE, TRASIE_output1 = TRASIE1, TRASIE_output2 = TRASIE2, TRASIE_output3 = TRASIE3, Tpars1 = Tpars1, Tpars2 = Tpars2, Tpars3 = Tpars3)
n_mainland_species <- 500 island_age <- 4 n_replicates <- 50 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, ext_rate * 0.1, island_wide_cap, imm_rate, ana_rate) ## great difference pars2 = c(clado_rate, ext_rate * 0.8, island_wide_cap, imm_rate, ana_rate) ## 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, ext_rate2 = ext_rate * 1.9, ana_rate2 = ana_rate, clado_rate2 = clado_rate, trans_rate2 = 0, M2 = n_mainland_species ) Tpars2 <- create_trait_state_params( trans_rate = 0, immig_rate2 = imm_rate, ext_rate2 = ext_rate * 1.2, ana_rate2 = ana_rate, clado_rate2 = clado_rate, trans_rate2 = 0, 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, 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 = TRASIE3,Tpars = Tpars3, use_dev_new = FALSE)
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