Nothing
## ----setup_params-------------------------------------------------------------
spec_matrix <- c(0, 0, 0, 1)
spec_matrix <- rbind(spec_matrix, c(1, 1, 1, 1))
lambda_list <- secsse::create_lambda_list(state_names = c(0, 1),
num_concealed_states = 2,
transition_matrix = spec_matrix,
model = "CR")
mu_vector <- secsse::create_mu_vector(state_names = c(0, 1),
num_concealed_states = 2,
model = "CR",
lambda_list = lambda_list)
shift_matrix <- c(0, 1, 3)
shift_matrix <- rbind(shift_matrix, c(1, 0, 4))
q_matrix <- secsse::create_q_matrix(state_names = c(0, 1),
num_concealed_states = 2,
shift_matrix = shift_matrix,
diff.conceal = FALSE)
## ----enter parameters---------------------------------------------------------
speciation_rate <- 0.5
extinction_rate <- 0.05
q_ab <- 0.1
q_ba <- 0.1
used_params <- c(speciation_rate, extinction_rate, q_ab, q_ba)
sim_lambda_list <- secsse::fill_in(lambda_list, used_params)
sim_mu_vector <- secsse::fill_in(mu_vector, used_params)
sim_q_matrix <- secsse::fill_in(q_matrix, used_params)
## ----simulate_tree------------------------------------------------------------
sim_tree <- secsse::secsse_sim(lambdas = sim_lambda_list,
mus = sim_mu_vector,
qs = sim_q_matrix,
crown_age = 5,
num_concealed_states = 2,
seed = 5)
if (requireNamespace("diversitree")) {
traits_for_plot <- data.frame(trait = as.numeric(sim_tree$obs_traits),
row.names = sim_tree$phy$tip.label)
diversitree::trait.plot(tree = sim_tree$phy,
dat = traits_for_plot,
cols = list("trait" = c("blue", "red")),
type = "p")
} else {
plot(sim_tree$phy)
}
## ----conditioning-------------------------------------------------------------
sim_tree <- secsse::secsse_sim(lambdas = sim_lambda_list,
mus = sim_mu_vector,
qs = sim_q_matrix,
crown_age = 5,
num_concealed_states = 2,
conditioning = "obs_states",
seed = 6)
sim_tree$obs_traits
sim_tree$true_traits
sim_tree <- secsse::secsse_sim(lambdas = sim_lambda_list,
mus = sim_mu_vector,
qs = sim_q_matrix,
crown_age = 5,
num_concealed_states = 2,
conditioning = "true_states",
seed = 6)
sim_tree$obs_traits
sim_tree$true_traits
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