sim.morpho  R Documentation 
Generates a morphological matrix using rTraitDisc
or gen.seq.HKY
functions.
sim.morpho(
tree,
characters,
states = 1,
model = "ER",
rates,
substitution = c(stats::runif, 2, 2),
invariant = TRUE,
verbose = FALSE
)
tree 
A phylogenetic tree to use for generating the characters. 
characters 
The number of morphological characters to generate. 
states 
A 
model 
Either an implemented ( 
rates 
A function an its parameters for the rates distribution (see details). 
substitution 
A function an its parameters for the substitutions distribution (see details; 
invariant 

verbose 
Whether to be verbose or not ( 
The model
arguments must be either a user's defined function for generating the discrete morphological characters (that takes the states, rates and substitution arguments) or one of the two following:
"ER"
uses the ape::rTraitDisc
function with the "ER"
model argument (= Mk model).
"HKY"
uses the phyclust::gen.seq.HKY
function with kappa
sampled from the substitution
argument, pi = runif(4)
(divided by sum(runif(4))
), rate.scale
sampled from the rates
distribution and L
being the number of characters
and transforms the purines (A, G) into 0 and the pyrimidines (C, T) into 1.
"MIXED"
randomly uses "ER"
or "HKY"
for binary characters and "ER"
for any character with more than two states.
the user defined model must be a function
that generates a single discrete morphological character and takes one element from at least the following arguments: tree
, states
, rates
, substitution
.
The states
argument attributes a number of states to each character by using the given probability vector for each number of states starting from two.
For example states = c(0.7, 0.2, 0.1)
will generate 70% of characters with two states, 20% of characters with three states and 10% of characters with four states.
The rates
and substitution
arguments require a function that outputs a distribution and its optional parameters. For example rates = c(runif, 1, 10)
creates a uniform distribution between 1 and 10 for the rates distribution.
Thomas Guillerme
check.morpho
, apply.NA
, rTraitDisc
, gen.seq.HKY
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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