tree_add_dates: Add missing taxa to a dated tree and fabricate node ages for...

In datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

Add missing taxa to a dated tree and fabricate node ages for these missing taxa.

Description

This function adds missing taxa to a chronogram given in dated_tree. It is still work in progress.

Usage

tree_add_dates(
  dated_tree = NULL,
  missing_taxa = NULL,
  dating_method = "mrbayes",
  adding_criterion = "random",
  mrbayes_output_file = "mrbayes_tree_add_dates.nexus"
)

Arguments

dated_tree	a tree (newick or phylo) with branch lengths proportional to absolute time
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.
dating_method	The method used for tree dating, options are "mrbayes" and "bladj".
adding_criterion	Only used when dating_method = "mrbayes". A character vector to specify how missing_taxa should be added to dated_tree. Choose one of: adding_method = "random" missing_taxa will be added at random to dated_tree. adding_method = "taxonomy" taxa will be added to dated_tree following a dataframe with taxonomic assignations given in missing_taxa argument. If no dataframe is given, OpenTree's reference taxonomy will be used. adding_method = "tree" taxa will be added to dated_tree following a tree given in missing_taxa argument. If no tree is given, OpenTree's synthetic tree will be used.
mrbayes_output_file	A character vector specifying the name of mrBayes run file and outputs (can specify directory too).

Value

A phylo object.

datelife documentation built on July 10, 2023, 2:02 a.m.