Simulate functions on a ginven tree
sim_fun_on_tree(
tree,
tip.type,
node.type,
psi,
mu_d,
mu_s,
eta,
Pi,
P = 1L,
informative = getOption("aphylo_informative", FALSE),
maxtries = 20L
)
An object of class phylo
Integer vectors with values 0,1. 0 denotes duplication node and 1 speciation node. This is used in LogLike.
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
).
Integer scalar. Number of functions to simulate.
Logical scalar. When TRUE
(default) the function
re-runs the simulation algorithm until both 0s and 1s show in the leaf
nodes of the tree.
Integer scalar. If informative = TRUE
, then the function
will try at most maxtries
times.
An matrix of size length(offspring)*P
with values 9, 0 and 1
indicating "no information"
, "no function"
and "function"
.
Using the model described in the vignette peeling_phylo.html
The optiona informative
was created such that when needed the
function can be forced to simualte annotations while making sure (or at
least trying maxtries
times) that the leafs have both 0s and 9s. From what
we've learned while conducting simulation studies, using this option may
indirectly bias the data generating process.
# Example 1 ----------------------------------------------------------------
# We need to simulate a tree
set.seed(1231)
newtree <- sim_tree(1e3)
# Preprocessing the data
# Simulating
ans <- sim_fun_on_tree(
newtree,
psi = c(.01, .05),
mu_d = c(.90, .80),
mu_s = c(.1, .05),
Pi = .5,
eta = c(1, 1)
)
# Tabulating results
table(ans)
#> ans
#> 0 1
#> 951 1048