simulate_internal: Simulate a Stochastic Process on a tree

In pbastide/PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM

Simulate a Stochastic Process on a tree

Description

simulate_internal simulate a stochastic process on a tree.

Usage

simulate_internal(
  phylo,
  process = c("BM", "OU", "scOU", "OUBM", "StudentOU"),
  p = 1,
  root.state = list(random = FALSE, stationary.root = FALSE, value.root = NA, exp.root =
    NA, var.root = NA),
  shifts = list(edges = NULL, values = NULL, relativeTimes = NULL),
  eps = 10^(-6),
  selection.strength = NULL,
  variance = NULL,
  optimal.value = NULL,
  checks = TRUE,
  simulate_random = TRUE,
  U_tree = NULL,
  times_shared = NULL,
  df = 1
)

Arguments

phylo	a phylogenetic tree, class phylo.
process	The model used for the simulation. One of "BM" (for a full BM model, univariate or multivariate); "OU" (for a full OU model, univariate or multivariate); or "scOU" (for a "scalar OU" model).
p	Dimension of the simulated trait
root.state	List describing the state of the root, with: random random state (TRUE) or deterministic state (FALSE) value.root if deterministic, value of the character at the root exp.root if random, expectation of the character at the root var.root if random, variance of the character at the root (pxp matrix)
shifts	List with position and values of the shifts : edges vector of the K id of edges where the shifts are values matrix p x K of values of the shifts on the edges (one column = one shift) relativeTimes vector of dimension K of relative time of the shift from the parent node of edges
eps	Tolerance for the value of the norm 1 of the selection strength matrix for OU
selection.strength	Matrix of selection strength size p x p (OU)
variance	Variance-covariance matrix size p x p
optimal.value	Vector of p optimal values at the root (OU)
checks	whether to check the entry parameters for consistency. Default to TRUE.
simulate_random	set to FALSE if only the expected values are needed (and not the random sample). Default to TRUE.
U_tree	optional, full incidence matrix of the tree, result of function incidence.matrix.full.
times_shared	optional, times of shared ancestry of all nodes and tips, result of function compute_times_ca. Can be specified to avoid extra computations.
df	if the process is "StudentOU", the number of degree of freedom of the chosen student law. default to 1.

Value

paramSimu An array with dimensions p x Nnode x 2 (BM) or p x Nnode x 3 (OU). For each trait t, 1 <= t <= p, paramSimu[t, , ] has tree columns, containing respectively the simulated state, expected value and optimal value for all the nodes.

pbastide/PhylogeneticEM documentation built on Feb. 12, 2024, 1:27 a.m.