treeDater: Rboretum Tree Dater

In BobLiterman/Rboretum: Compare Phylogenetic Trees and Alignment Support Values

Rboretum Tree Dater

Description

This function takes a tree(s) with estimated branch lengths, and returns ultrametric chronograms generated using the 'chronos' function in 'ape'

Usage

treeDater(tree, calibration_df, taxa, min_max, iterations)

Arguments

tree	Tree(s) to extract date information from. Options include: A single, rooted phylo object; or, A rooted multiPhylo object where all trees support a single topology
calibration_df	A 4-column dataframe/tibble with calibration information: (1) Taxon 1 (2) Taxon 2 [to get MRCA] (3) Min divergence time (4) Max divergence time; Multiple calibration points are allowed, so long as nodes are only calibrated once [Supercedes 'taxa' argument]
taxa	A character vector (or semicolon-delimited set) of taxon IDs from which to find the MRCA and calibrate [One calibration point allowed; Superceded by 'calibration_df']
min_max	If using 'taxa', a two-element numeric vector [e.g. c(50,75)] that provides the minimum and maximum age estimates for the focal calibration node [Superceded by 'calibration_df'; min <= max]
iterations	How many times to estimate the age of each node prior to summarizing [Default: 1000]

Value

An ultrametric phylo object with branch lengths corresponding to time, or a multiPhylo of such trees.

BobLiterman/Rboretum documentation built on July 6, 2023, 7:46 p.m.