R: Create an object 'params_process' for an OU

params_OU {PhylogeneticEM} | R Documentation

## Create an object `params_process` for an OU

### Description

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

### 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 strength 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` | whether 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 (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.
`...` | unused.

### Value

an object of class `params_process`.

### See Also

`params_process`, `params_BM`

[Package PhylogeneticEM version 1.1.0 Index]