Usage
simulate_internal(phylo, process = c("BM", "OU", "scOU", "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
Dimention of the simulated trait
root.state
List describing the state of the root, with:
shifts
List with position and values of the shifts :
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 precised to avoid extra
computations. df
if the process is "StudentOU", the number of degree of freedom of
the choosen student law. default to 1.