Usage
params_OU(p = 1, variance = diag(1, p, p), selection.strength = diag(1, p, p), optimal.value = rep(0, p), random = TRUE, stationary.root = TRUE, value.root = rep(0, p), exp.root = rep(0, p), var.root = diag(1, p, p), edges = NULL, values = matrix(0, p, length(edges)), relativeTimes = NULL, nbr_of_shifts = length(edges), phylo = NULL, ...)
Arguments
p
the dimension (number of traits) of the parameters. Default to 1.
variance
the variance (rate matrix) of the BM. Default to
diag(1, p, p).
selection.strength
the selection strenght matrix. Default to
diag(1, p, p).
optimal.value
the vector of the optimal values at the root. Default
to rep(0, p).
random
whether the root of the OU is random (TRUE) or fixed (FALSE).
Default to TRUE.
stationary.root
wheter the root of the OU is stationary (TRUE) or not.
Default to TRUE.
value.root
if random=FALSE, the root value. Default to 0.
exp.root
if random=TRUE, the root expectation. Default to 0. If
stationary.root=TRUE, default to optimal.value.
var.root
if random=TRUE, the root variance. Default to
diag(1, p, p). If stationary.root=TRUE, default to
the stationary variance computed from variance and
selection.strength, see function
compute_stationary_variance. edges
a vector of edges where the shifts occur. Default to NULL
(no shift).
values
a matrix of shift values, with p lines and as many columns as
the number of shifts. Each column is the p values for one shift. Default to
matrix(0, p, length(edges)).
relativeTimes
(unused) the relative position of the shift on the
branch, between 0 (begining of the branch) and 1 (end of the branch). Default
to 0.
nbr_of_shifts
the number of shifts to use (randomly drawn). Use only
if edges is not specified. In that case, a phylogenetic tree must be
provided (to allow a random sampling of its edges).
phylo
a phylogenetic tree of class phylo. Needed only if
the shifts edges are not specified.