Add missing taxa to a dated tree and fabricate node ages for these missing taxa.
Source:R/tree_add_dates.R
tree_add_dates.RdThis 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).