Get Lower Bound on sigma2_error

Find reasonable lower bound on the sigma2_error parameter when fitted with phylolm.

Usage

getMinError(phy, tol = (.Machine$double.eps)^0.5)

Arguments

phy

a phylogenetic tree.

tol

the numerical tolerance.

Value

The minimum value for sigma2_error.

Details

The minimum value must be high enough so that it can be numerically distinguished from zero. This is important for trees with several samples per species, as the limit case sigma2_error = 0 is degenerate, as it means that all the samples in one species have the exact same value.

Default to \(tol * h\), where \(h\) is the total height of the tree. Note that if an OU is used in the fit, then this value is updated to match the transformed tree height.