raphylo function

Simulation of Annotated Phylogenetic Trees

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 or 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

Returns

An object of class aphylo

Details

The rmultiAphylo function is a wrapper around raphylo.

Examples

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

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