Manipulation and analysis of phylogenetically simulated
        data sets and phylogenetically based analyses using GLS.

Contains functions for developing phylogenetic trees as
    deeply-nested lists ("dendrogram" objects).
    Enables bi-directional conversion between dendrogram and
    "phylo" objects
    (see Paradis et al (2004) <doi:10.1093/bioinformatics/btg412>),
    and features several tools for command-line tree
    manipulation and import/export via Newick parenthetic text.

Provides functions for fitting phylogenetic linear models and phylogenetic generalized linear models. The computation uses an algorithm that is linear in the number of tips in the tree. The package also provides functions for simulating continuous or binary traits along the tree. Other tools include functions to test the adequacy of a population tree.

Provides functions to estimate statistical errors of phylogenetic
    metrics particularly to detect binary trait influence on diversification, as
    well as a function to simulate trees with fixed number of sampled taxa and trait
    prevalence.

A comprehensive and easy to use R implementation of confirmatory
    phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer
    (2012) <doi:10.1111/j.1558-5646.2012.01790.x>.

Phylogenetic Diversity (PD, Faith 1992), Evolutionary Distinctiveness (ED, Isaac et al. 2007), Phylogenetic Endemism (PE, Rosauer et al. 2009; Laffan et al. 2016), and Weighted Endemism (WE, Laffan et al. 2016) for presence-absence raster.
    Faith, D. P. (1992) <doi:10.1016/0006-3207(92)91201-3>
    Isaac, N. J. et al. (2007) <doi:10.1371/journal.pone.0000296>
    Laffan, S. W. et al. (2016)  <doi:10.1111/2041-210X.12513>
    Rosauer, D. et al. (2009) <doi:10.1111/j.1365-294X.2009.04311.x>.

Computational infrastructure for biogeography, community ecology,
    and biodiversity conservation (Daru et al. 2020) <doi:10.1111/2041-210X.13478>.
    It is based on the methods described in Daru et al. (2020) <doi:10.1038/s41467-020-15921-6>.
    The original conceptual work is described in Daru et al. (2017) <doi:10.1016/j.tree.2017.08.013>
    on patterns and processes of biogeographical regionalization. Additionally, the package
    contains fast and efficient functions to compute more standard conservation measures
    such as phylogenetic diversity, phylogenetic endemism, evolutionary distinctiveness
    and global endangerment, as well as compositional turnover (e.g., beta diversity).