tree_add_dates: Fabricates dates of missing taxa (with no data) on an already...

Description Usage Arguments Value

View source: R/tree_makeup_dates.R

Description

Fabricates dates of missing taxa (with no data) on an already dated tree.

Usage

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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. 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.

dating_method

The method used for tree dating.

adding_criterion

Only valid 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, OToLs 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, OToL 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


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