set.seed(4)
## A random tree with 15 tips
tree <- rcoal(15)
## Setting up the parameters
my_rates = c(rgamma, rate = 10, shape = 5)
my_substitutions = c(runif, 2, 2)
## HKY binary (15*50)
matrixHKY <- sim.morpho(tree, characters = 50, model = "HKY",
rates = my_rates, substitution = my_substitutions)
## Mk matrix (15*50) (for Mkv models)
matrixMk <- sim.morpho(tree, characters = 50, model = "ER", rates = my_rates)
## Mk invariant matrix (15*50) (for Mk models)
matrixMk <- sim.morpho(tree, characters = 50, model = "ER", rates = my_rates,
invariant = FALSE)
## MIXED model invariant matrix (15*50)
matrixMixed <- sim.morpho(tree, characters = 50, model = "MIXED",
rates = my_rates, substitution = my_substitutions, invariant = FALSE,
verbose = TRUE)
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