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. 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: |
0.3.1 |
| Depends: |
R (≥ 4.1.0) |
| Imports: |
ape, parallel, Rcpp, stats |
| LinkingTo: |
Rcpp, RcppArmadillo |
| Suggests: |
caper, mvtnorm, phytools, testthat |
| Published: |
2026-10-27 |
| DOI: |
10.32614/CRAN.package.fastphylosig (may not be active yet) |
| 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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