prep_branch_lengths: Prepare branches for HRF calculation
In guerreror/pepo: Estimate Hemiplasy and Homoplasy on a Phylogeny

Take a 'phylo' object and extract the relevant branches for each HRF calculation.

Optionally, adjust the tip length values (if 'tip_replace' is not NULL). Because estimating branch length at tips is impossible for coalescent methods, some implementations (like MP-EST) return tips of arbitrary length. These lengths don't have biological meaning but can affect the value of HRF. This function changes the values of the tips for another, equally arbitrary length.

If 'tip_replace' is a single value, it's applied to all tips. If 'tip_replace' is a vector, it will be passed directly to all tips (it needs to be of length equal to number of tips).

If 'tip_replace' is a phylogeny (an object of class 'phylo'), the replacement values will be extrapolated from the correlation of the two sets of branch lengths (the ones given in 'tree' and the ones in 'tip_replace'), excluding the tips. This method assumes that the nodes in the 'tip_replace' phylogeny are in the same order as in 'tree'. While not mandatory, it is strongly recommended that the topologies of the two trees are the identical.

If 'concordance_factors' is not NULL, it'll modify branch lengths using concordance factors. If 'concordance_factors' is a character, it'll be taken as the name of the variable in the data frame that corresponds to the concordance factors. If it's a numeric vector, it'll be taken as the values of concordance factors (in the same order as the corresponding branches in the data frame).

1 2	prep_branch_lengths(tree, tip_replace = NULL, concordance_factors = NULL)

`tree`	a phylogeny of class 'phylo'
`tip_replace`	NULL(default), numeric of length 1, or numeric vector of length equal to number of tips, or object of class 'phylo'.
`concordance_factors`	NULL(default), character, numeric vector of length equal to number of branches in tree