This repository adds a package structure to BeastMasteR, allowing the code to be installed with
# Install required packages if necessary
install.packages("XML")
install.packages("devtools")
# Then install BeastMasteR
devtools::install_github("ms609/BeastMasteR") # case sensitiveThe purpose of "BEASTmasteR" is to convert NEXUS data file(s) (DNA, amino acids, discrete morphological characters, and/or continuous traits), plus an Excel settings file, into Beast2 XML format.
The author is Nicholas J. Matzke, ORCID: http://orcid.org/0000-0002-8698-7656 .
BEASTmasteR is primarily aimed at enabling tip-dating analyses using fossils as dated terminal taxa. The Birth-Death-Skyline-Serial-Sampling tree model is used (or the Sampled-Ancestors variant), enabling different birth, death, and sampling rates through time. However, it may be useful for setting up molecular-only analyses (particularly automated variants), for learning Beast2 XML (since the BEASTmasteR XML output is annotated and much easier for human reading than the BEAUTi output), or for automating such analyses. BEASTmasteR also contains functions for parsing Beast2 output, e.g. plotting a dated tree in R, with posterior probabilities, 95% HPDs on node dates, and also 95% HPDs on tip dates, if available.
2016-2017 additions: Added ascertainment bias corrections, various bug checks, gene-tree/species tree analysis setup.
Citation
BEASTmasteR will eventually become an R package and have a publication associated with it. Until then, please cite something like:
Matzke, Nicholas J. (2017). "BEASTmasteR: R tools for automated conversion of NEXUS data to BEAST2 XML format, for fossil tip-dating and other uses." Instructions at PhyloWiki, http://phylo.wikidot.com/beastmaster. Accessed (access date).
Matzke, Nicholas J. (2017). BEASTmasteR code archive. Github: https://github.com/nmatzke/BEASTmasteR . Accessed (access date). Release: XX. DOI: XX.
Ideally, there will be a release with a DOI, but it may be you just use the
most up-to-date commit. Find the most recent release at:
https://github.com/nmatzke/BEASTmasteR/releases , and/or DOI
http://dx.doi.org/10.5281/zenodo.31927 -- and a button:
Acknowledgements
Some of the functions in "tree_utils_v1.R", e.g. read_beast_prt, used for extracting the bracketed statistics from BEAST NEXUS tree files (MCC files) are copied/lightly modified/heavily modified from the R package " phyloch", by Christoph Heibl, licensed under GPL (>=2), available at: http://www.christophheibl.de/Rpackages.html. Please cite phyloch also, also if you use this feature.