Package: rtrees Title: Deriving Phylogenies from Synthesis Trees Version: 2.0.2 Authors@R: person(given = "Daijiang", family = "Li", role = c("aut", "cre"), email = "daijianglee@gmail.com", comment = c(ORCID = "0000-0002-0925-3421")) Description: 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) 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. License: GPL-3 Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) 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 URL: https://daijiang.github.io/rtrees/ VignetteBuilder: knitr, R.rsp Config/roxygen2/version: 8.0.0 Config/pak/sysreqs: cmake make libicu-dev libuv1-dev Repository: https://daijiang.r-universe.dev Date/Publication: 2026-06-05 15:39:39 UTC RemoteUrl: https://github.com/daijiang/rtrees RemoteRef: HEAD RemoteSha: 82bd94d32b49f380ccff1a8646e77abafaef2ae1 NeedsCompilation: yes Packaged: 2026-06-29 11:11:55 UTC; root Author: Daijiang Li [aut, cre] (ORCID: ) Maintainer: Daijiang Li