get_mrbayes_node_constraints: Makes a block of node constraints and node calibrations for a MrBayes run file from a list of taxa and ages, or from a dated tree

Description

Makes a block of node constraints and node calibrations for a MrBayes run file from a list of taxa and ages, or from a dated tree

Usage

get_mrbayes_node_constraints(
  constraint = NULL,
  taxa = NULL,
  missing_taxa = NULL,
  ncalibration = NULL,
  age_distribution = "fixed",
  root_calibration = FALSE,
  mrbayes_constraints_file = NULL,
  clockratepr = "prset clockratepr = fixed(1);"
)

Value

A set of MrBayes constraints and/or calibration commands printed in console as character strings or as a text file specified in mrbayes_constraints_file.

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

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.

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.

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_constraints_file

NULL or a character vector indicating the name of mrbayes constraint and/or calibration block file.

clockratepr

A character vector indicating the clockrateprior to be used.