Take a constraint tree and use mrBayes to get node ages and branch lengths given a set of node calibrations without any data.

Usage

make_mrbayes_tree(
  constraint = NULL,
  taxa = NULL,
  ncalibration = NULL,
  missing_taxa = NULL,
  age_distribution = "fixed",
  root_calibration = FALSE,
  mrbayes_output_file = "mrbayes_run.nexus"
)

Arguments

constraint

The constraint tree: a phylo object or a newick character string, with or without branch lengths.

taxa

A character vector with taxon names to be maintained in tree

ncalibration

The node calibrations: a phylo object with branch lengths proportional to time; in this case all nodes from ncalibration will be used as calibration points. Alternatively, a list with two elements: the first is a character vector with node names from phy to calibrate; the second is a numeric vector with the corresponding ages to use as calibrations.

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.

age_distribution

A character string specifying the type of calibration. Only "fixed" and "uniform" are implemented for now.

fixed: The age given in ncalibration will be used as fixed age.
lognormal: The age given in ncalibration will be used as mean age. The standard deviation can be provided. # still need to add this option. By default, a 95 CI sd is used.
uniform: The age given in ncalibration will be used as mean age. Where min_age = 0.9 * mean age, and max_age = 1.1 * mean age.

root_calibration

Used to set a calibration at the root or not. Default to FALSE. Only relevant if ncalibration is specified.

mrbayes_output_file

A character vector specifying the name of mrBayes run file and outputs (can specify directory too).

Value

A phylo object with branch lengths proportional to time. It saves all mrBayes outputs in the working directory.