View source: R/make_mrbayes_tree.R
make_mrbayes_tree | R Documentation |
Take a constraint tree and use mrBayes to get node ages and branch lengths given a set of node calibrations without any data.
make_mrbayes_tree(
constraint = NULL,
taxa = NULL,
ncalibration = NULL,
missing_taxa = NULL,
age_distribution = "fixed",
root_calibration = FALSE,
mrbayes_output_file = "mrbayes_run.nexus"
)
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.
|
age_distribution |
A character string specifying the type of calibration. Only "fixed" and "uniform" are implemented for now.
|
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). |
A phylo
object with branch lengths proportional to time. It saves all
mrBayes outputs in the working directory.
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