Package: fastphylosig
Type: Package
Title: Fast Phylogenetic Signal Statistics
Version: 0.3.5
Authors@R: 
    person("Yin", "Wen", role = c("aut", "cre"),
           email = "wenyinsci@126.com")
Description: Provides one-command and method-specific workflows for
    phylogenetic signal in continuous, binary, and categorical traits. Compiled
    tree-pruning algorithms implement Blomberg's K and Pagel's lambda without
    constructing a dense phylogenetic covariance matrix in production.
    Fritz and Purvis D retains separate random and Brownian null models, while
    categorical Delta combines discrete ancestral-state likelihoods with MCMC
    and permutation diagnostics. The package also provides reusable prepared
    trees, explicit tree/data matching, trait-wise missing-value handling,
    conservative tree diagnostics, bounded simulation memory, and structured
    timing and Monte Carlo uncertainty metadata. Clade scans describe local
    and overall signal in continuous, binary and multistate traits, with
    optional model-reference tests of signal dispersion or deviation. Methods
    follow Blomberg, Garland and Ives (2003)
    <doi:10.1111/j.0014-3820.2003.tb00285.x> for K, Pagel (1999)
    <doi:10.1038/44766> for lambda, Fritz and Purvis (2010)
    <doi:10.1111/j.1523-1739.2010.01455.x> for D, and Borges et al. (2019)
    <doi:10.1093/bioinformatics/bty800> for categorical Delta.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: ape, parallel, Rcpp, stats
LinkingTo: Rcpp, RcppArmadillo
Suggests: caper, expm, mvtnorm, phytools, testthat
URL: https://github.com/yinwen-ecology/fastphylosig,
        https://yinwen-ecology.github.io/fastphylosig/
BugReports: https://github.com/yinwen-ecology/fastphylosig/issues
SystemRequirements: C++17, OpenMP (optional)
Config/testthat/edition: 3
NeedsCompilation: yes
Config/roxygen2/version: 8.1.0
Packaged: 2026-11-01 08:15:36 UTC; agent
Author: Yin Wen [aut, cre]
Maintainer: Yin Wen <wenyinsci@126.com>
Repository: CRAN
Date/Publication: 2026-11-02 16:20:10 UTC
