params_BM: Create an object 'params_process' for a BM

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

Create an object params_process for a BM

Description

params_BM creates a coherent object params_process from user provided values of the parameters. Non specified parameters are set to default values.

Usage

params_BM(
  p = 1,
  variance = diag(1, p, p),
  random = FALSE,
  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,
  sBM_variance = FALSE,
  trait_names = 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).
random	whether the root of the BM is random (TRUE) or fixed (FALSE). Default to FALSE.
value.root	if random=FALSE, the root value. Default to 0.
exp.root	if random=TRUE, the root expectation. Default to 0.
var.root	if random=TRUE, the root variance. Default to diag(1, p, p).
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 (beginning 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, or if sBM_variance=TRUE. Default to NULL. If sBM_variance=TRUE, it must have a specified value for the root branch length (slot root.edge).
sBM_variance	if the root is random, does it depend on the length of the root edge ? (For equivalent purposes with a rescaled OU). Default to FALSE. If TRUE, a phylogenetic tree with root edge length must be provided.
trait_names	vector of trait names values. Must be of length p.
...	unused.

Value

an object of class params_process.

See Also

params_process, params_OU

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