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) <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.
License: GPL-3
Encoding: UTF-8
LazyData: 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
NeedsCompilation: yes
Packaged: 2026-06-05 15:40:11 UTC; dli
Author: Daijiang Li [aut, cre] (ORCID: <https://orcid.org/0000-0002-0925-3421>)
Maintainer: Daijiang Li <daijianglee@gmail.com>
Repository: CRAN
Date/Publication: 2026-06-11 11:40:07 UTC
