find_grid_alpha: Find a reasonable grid for alpha

In pbastide/PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM

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, with t_1/2 the phylogenetic half life: t_1/2 = log(2)/alpha. 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,
  allow_negative = FALSE,
  ...
)

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.
allow_negative	whether to allow negative values for alpha (Early Burst). See documentation of PhyloEM for more details. Default to FALSE.
...	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

pbastide/PhylogeneticEM documentation built on Feb. 12, 2024, 1:27 a.m.