rtrees: Deriving Phylogenies from Synthesis Trees
Provides tools to derive species-level phylogenies from large synthesis mega-trees for a wide range of taxonomic groups, including plants, birds, mammals, amphibians, reptiles, fish, bees, butterflies, and sharks. When a queried species is absent from the mega-tree, it is grafted onto the tree using one of two placement strategies: attachment at the basal node of the most closely related genus or family ('at_basal_node'), or random attachment below that basal node with probability proportional to branch length ('random_below_basal'). See Li (2023) <doi:10.1111/ecog.06643> for details. Multiple species from a genus not represented in the mega-tree are placed as a polytomy to preserve clade coherence. The package interfaces with the 'megatrees' data package, which bundles or downloads on demand curated mega-trees. Users can also provide their own mega-trees.
| Version: | 2.0.2 |
| Depends: | R (≥ 3.5.0) |
| Imports: | ape, tidytree, dplyr, tibble, utils, castor, furrr, future, megatrees (≥ 0.1.3), fastmatch, data.table, Rcpp |
| LinkingTo: | Rcpp |
| Suggests: | knitr, rmarkdown, testthat, piggyback, R.rsp, ggplot2 |
| Published: | 2026-06-11 |
| DOI: | 10.32614/CRAN.package.rtrees (may not be active yet) |
| Author: | Daijiang Li  [aut,
cre] |
| Maintainer: | Daijiang Li <daijianglee at gmail.com> |
| License: | GPL-3 |
| URL: | https://daijiang.github.io/rtrees/ |
| NeedsCompilation: | yes |
| Citation: | rtrees citation info |
| Materials: | README |
| CRAN checks: | rtrees results |
Documentation:
| Reference manual: | rtrees.html , rtrees.pdf |
| Vignettes: |
Speed comparisons (source, R code) Non-monophyletic-groups (source) Simple_example (source) grafting_scenarios (source) |
Downloads:
| Package source: | rtrees_2.0.2.tar.gz |
| Windows binaries: | r-devel: rtrees_2.0.2.zip, r-release: not available, r-oldrel: rtrees_2.0.2.zip |
| macOS binaries: | r-release (arm64): rtrees_2.0.2.tgz, r-oldrel (arm64): rtrees_2.0.2.tgz, r-release (x86_64): rtrees_2.0.2.tgz, r-oldrel (x86_64): rtrees_2.0.2.tgz |
Linking:
Please use the canonical form https://CRAN.R-project.org/package=rtrees to link to this page.