raphylo {aphylo}

Simulation of Annotated Phylogenetic Trees

Description

Simulation of Annotated Phylogenetic Trees

Usage

raphylo(
  n = NULL,
  tree = NULL,
  edge.length = NULL,
  tip.type = NULL,
  node.type = function(n) sample.int(2, size = n, replace = TRUE, prob = c(0.2, 0.8)) - 1,
  P = 1L,
  psi = c(0.05, 0.05),
  mu_d = c(0.9, 0.5),
  mu_s = c(0.05, 0.02),
  eta = c(1, 1),
  Pi = 0.2,
  informative = getOption("aphylo_informative", FALSE),
  maxtries = 20L
)

rmultiAphylo(R, ...)

Arguments

n

Integer scalar. Number of leafs. If not specified, then

tree

An object of class phylo.

edge.length

Passed to sim_tree.

tip.type, node.type

Integer vectors with values 0,1. 0 denotes duplication node and 1 speciation node. This is used in LogLike.

P

Integer scalar. Number of functions to generate.

psi

Numeric vector of length 2. Misclasification probabilities. (see LogLike).

mu_d, mu_s

Numeric vector of length 2. Gain/loss probabilities (see LogLike).

eta

Numeric vector of length 2. Annotation bias probabilities (see LogLike).

Pi

Numeric scalar. Root node probability of having the function (see LogLike).

informative, maxtries

Passed to sim_fun_on_tree.

R

Integer, number of replicates

...

Further arguments passed to raphylo

Details

The rmultiAphylo function is a wrapper around raphylo.

Value

An object of class aphylo

Examples

# A simple example ----------------------------------------------------------

set.seed(1231)
ans <- raphylo(n=500)