getBoundsSelectionStrength: Get Bounds on alpha

In pbastide/phylolimma: Phylogenetic Comparative Methods for limma

Get Bounds on alpha

Description

Find reasonable bounds on the alpha parameter.

Usage

getBoundsSelectionStrength(
  phy,
  relative_half_life_min = 1e-04,
  relative_half_life_max = 10000
)

Arguments

phy	a phylogenetic tree.
relative_half_life_min	optional minimal half life relative to tree height
relative_half_life_max	optional maximal half life relative to tree height

Details

This functions tries to find reasonable bounds on the \alpha parameter of an OU process by using the scaled phylogenetic half-life t_{1/2} = \log(2) / \alpha / h, where h is the total height of the tree. If t_{1/2} = D), it means that the trait will need a time D \times h to cover half the distance to the optimal value (see Hansen, 1997). Small values of D means high selection pressure (large \alpha), while large values of D means low selection pressure (small \alpha).

The default maximum value for D is relative_half_life_max = 10000 (selection is week and the process looks like a BM).

The default minimum value for D is relative_half_life_min = 0.0001 (selection is strong and tips are only weakly correlated).

The function makes sure that the maximum \alpha value associated with relative_half_life_min does not lead to underflow errors when rescaling the tree.

Value

A vector with lower and upper bounds for alpha

References

Hansen, T. F. (1997). Stabilizing Selection and the Comparative Analysis of Adaptation. Evolution, 51(5) :1341.

pbastide/phylolimma documentation built on Nov. 17, 2024, 1:34 p.m.