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
Source:R/make_mrbayes_tree.R
get_mrbayes_node_constraints.RdMakes 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);"
)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.