fastphylosig: Fast Phylogenetic Signal Statistics
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.
| Version: |
0.3.5 |
| Depends: |
R (≥ 4.1.0) |
| Imports: |
ape, parallel, Rcpp, stats |
| LinkingTo: |
Rcpp, RcppArmadillo |
| Suggests: |
caper, expm, mvtnorm, phytools, testthat |
| Published: |
2026-11-02 |
| DOI: |
10.32614/CRAN.package.fastphylosig |
| Author: |
Yin Wen [aut, cre] |
| Maintainer: |
Yin Wen <wenyinsci at 126.com> |
| BugReports: |
https://github.com/yinwen-ecology/fastphylosig/issues |
| License: |
MIT + file LICENSE |
| URL: |
https://github.com/yinwen-ecology/fastphylosig,
https://yinwen-ecology.github.io/fastphylosig/ |
| NeedsCompilation: |
yes |
| SystemRequirements: |
C++17, OpenMP (optional) |
| Materials: |
README, NEWS |
| CRAN checks: |
fastphylosig results |
Documentation:
Downloads:
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