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Methods and workflows to get chronograms (i.e., phylogenetic trees with branch lengths proportional to time), using open, peer-reviewed, state-of-the-art scientific data on time of lineage divergence. This package constitutes the main underlying code of the DateLife web service at <https://www.datelife.org>. To obtain a single summary chronogram from a group of relevant chronograms, we implement the Super Distance Matrix (SDM) method described in Criscuolo et al. (2006) <doi:10.1080/10635150600969872>. To find the grove of chronograms with a sufficiently overlapping set of taxa for summarizing, we implement theorem 1.1. from Ané et al. (2009) <doi:10.1007/s00026-009-0017-x>. A given phylogenetic tree can be dated using time of lineage divergence data as secondary calibrations (with caution, see Schenk (2016) <doi:10.1371/journal.pone.0148228>). To obtain and apply secondary calibrations, the package implements the congruification method described in Eastman et al. (2013) <doi:10.1111/2041-210X.12051>. Tree dating can be performed with different methods including BLADJ (Webb et al. (2008) <doi:10.1093/bioinformatics/btn358>), PATHd8 (Britton et al. (2007) <doi:10.1080/10635150701613783>), mrBayes (Huelsenbeck and Ronquist (2001) <doi:10.1093/bioinformatics/17.8.754>), and treePL (Smith and O'Meara (2012) <doi:10.1093/bioinformatics/bts492>).
| Version: | 0.6.8 |
| Depends: | R (≥ 3.6.0) |
| Imports: | ape, abind, bold, phangorn, phytools, ips, cluster, compare, geiger, stats, stringr, rotl, paleotree, knitcitations, phylobase, taxize, treebase, utils, httr, plyr, phylocomr, BiocManager, data.table, curl |
| Suggests: | testthat, knitr, rmarkdown, usethis, devtools, covr, msa, Biostrings |
| Published: | 2023-06-19 |
| Author: | Brian O'Meara [aut], Jonathan Eastman [aut], Tracy Heath [aut], April Wright [aut], Klaus Schliep [aut], Scott Chamberlain [aut], Peter Midford [aut], Luke Harmon [aut], Joseph Brown [aut], Matt Pennell [aut], Mike Alfaro [aut], Luna L. Sanchez Reyes [aut, cre], Emily Jane McTavish [ctb] |
| Maintainer: | Luna L. Sanchez Reyes <sanchez.reyes.luna at gmail.com> |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: | https://github.com/phylotastic/datelife, http://phylotastic.org/datelife/ |
| NeedsCompilation: | no |
| SystemRequirements: | PATHd8 |
| Citation: | datelife citation info |
| Materials: | README NEWS |
| CRAN checks: | datelife results |
| Reference manual: | datelife.pdf |
| Vignettes: |
Getting started Case study: the true finches make_datelife_query making_bold_trees |
| Package source: | datelife_0.6.8.tar.gz |
| Windows binaries: | r-devel: datelife_0.6.8.zip, r-release: datelife_0.6.8.zip, r-oldrel: datelife_0.6.8.zip |
| macOS binaries: | r-release (arm64): datelife_0.6.8.tgz, r-oldrel (arm64): datelife_0.6.8.tgz, r-release (x86_64): datelife_0.6.8.tgz, r-oldrel (x86_64): datelife_0.6.8.tgz |
| Old sources: | datelife archive |
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These binaries (installable software) and packages are in development.
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