R: Find a reasonable grid for alpha

find_grid_alpha {PhylogeneticEM} | R Documentation

## Find a reasonable grid for alpha

### Description

Grid so that 2*ln(2)*quantile(d_ij)/factor_up_alpha < t_1/2 < factor_down_alpha * ln(2) * h_tree Ensures that for alpha_min, it is almost a BM, and for alpha_max, almost all the tips are decorrelated.

### Usage

    find_grid_alpha(phy, alpha = NULL, nbr_alpha = 10, factor_up_alpha = 2,
      factor_down_alpha = 3, quantile_low_distance = 1e-04,
      log_transform = TRUE, ...)

### Arguments

`phy` | phylogenetic tree of class "`phylo`"
`alpha` | fixed vector of alpha values if already known. Default to NULL.
`nbr_alpha` | the number of elements in the grid
`factor_up_alpha` | factor for up scalability
`factor_down_alpha` | factor for down scalability
`quantile_low_distance` | quantile for min distance
`log_transform` | whether to take a log scale for the spacing of alpha values. Default to TRUE.
`...` | not used.

### Details

If `quantile_low_distance=0`, then `quantile(d_ij)=min(d_ij)`, and, for any two tips i,j, the correlation between i and j is bounded by exp(-factor_up_alpha/2). Those values of alpha will be used for the re-scaling of the tree, which has an exponential term in exp(2*alpha*h). The function makes sure that this number is below the maximal float allowed (equals to `.Machine$double.xmax`).

### Value

A grid of alpha values

### See Also

`transform_branch_length`, `.Machine`

[Package PhylogeneticEM version 1.1.0 Index]