rrf.rates.times: Estimate relative lineage rates and node times.

In cathyqqtao/RRF: Relative Rate Framework in R

Description

This function estimates relative lineage rates and node times from a branch length tree using the relative rate framework (RRF).

Usage

rrf.rates.times(tree.name = "", outgroup = "", filename = "", plot = TRUE)

Arguments

tree.name	a file name of the branch length tree that is in the Newick format.
outgroup	a character list containing names of tips belonging to the rooting outgroup, which will be removed in the calculation. If outgroup = "" (the default), the input tree must be rooted and no tips will be removed.
filename	a file name specified for the output files.
plot	logical. If TRUE (default), the inferred timetree is plotted with the branches colored by the relative rates.

Value

A table of relative lineage rates and node times (<filename>_RRF_table.csv).

A timetree with branches colored by the relative rates (<filename>_RRF_timetree.nexus).

Author(s)

Qiqing Tao ([e-mail]) and Sudhir Kumar

References

K. Tamura et al. Mol. Biol. Evol. (2018) 35:1770-1782. doi:10.1093/molbev/msy044.

Examples

# Please download the "example.nwk" from https://github.com/cathyqqtao/RRF/tree/main/data.

rrf.rates.times(tree.name = "data/example.nwk", outgroup = c("Ornithorhynchus_anatinus", "Zaglossus_bruijni", "Tachyglossus_aculeatus"), filename = "data/example", plot = TRUE)

cathyqqtao/RRF documentation built on Dec. 19, 2021, 1:55 p.m.