missing_taxa_check: Checks that missing_taxa argument is ok to be used by...

Description Usage Arguments Value

View source: R/tree_makeup_dates.R

Description

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

Usage

1
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. taxon. A character vector of missing taxon names. clade. 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


phylotastic/datelife documentation built on Jan. 14, 2019, 9:56 p.m.