params_BM {PhylogeneticEM} | R Documentation |
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
|
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
|
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
|
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 |
phylo |
a phylogenetic tree of class |
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
.