R: Create an object 'params_process' for a BM

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, ...)

### 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.
`...` | unused.

### Value

an object of class `params_process`.

### See Also

`params_process`, `params_OU`

[Package PhylogeneticEM version 1.1.0 Index]