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, ...)
Integer scalar. Number of leafs. If not specified, then
An object of class phylo.
Passed to sim_tree.
Integer vectors with values 0,1. 0 denotes duplication node and 1 speciation node. This is used in LogLike.
Integer scalar. Number of functions to generate.
Numeric vector of length 2. Misclasification probabilities. (see LogLike
).
Numeric vector of length 2. Gain/loss probabilities (see LogLike
).
Numeric vector of length 2. Annotation bias probabilities (see LogLike
).
Numeric scalar. Root node probability of having the function (see LogLike
).
Passed to sim_fun_on_tree.
Integer, number of replicates
Further arguments passed to raphylo
An object of class aphylo
The rmultiAphylo
function is a wrapper around raphylo
.
# A simple example ----------------------------------------------------------
set.seed(1231)
ans <- raphylo(n=500)