missing_taxa_check {datelife}

Checks that missing_taxa argument is ok to be used by make_mrbayes_runfile inside tree_add_dates functions.

Description

Checks that missing_taxa argument is ok to be used by make_mrbayes_runfile inside tree_add_dates functions.

Usage

missing_taxa_check(missing_taxa = NULL, dated_tree = NULL)

Arguments

missing_taxa

A tree, a data frame or a vector enlisting all missing taxa you want to include.

A tree

Either as a phylo object or as a newick character string. It contains all taxa that you want at the end, both missing and non missing. This tree will be used as a hard constraint.

A data.frame

It contains two columns named "taxon" and "clade". The first one contains a character vector of missing taxon names. The second one contains a character or numeric vector of nodes from a constraint tree to which each taxon will be assigned.

A character vector

It contains the names of the missing taxa. They will be added at random to the constraint tree.

dated_tree

a tree (newick or phylo) with branch lengths proportional to absolute time

Value

A phylo object, a newick character string or a dataframe with taxonomic assignations