PhylogeneticEM (version 1.0.0)

find_grid_alpha: Find a reasonable grid for alpha

Description

Grid so that 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.

Value

A grid of alpha values