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phylopairs: Comparative Analyses of Lineage-Pair Traits

Facilitates the testing of causal relationships among lineage-pair traits in a phylogenetically informed context. Lineage-pair traits are characters that are defined for pairs of lineages instead of individual taxa. Examples include the strength of reproductive isolation, range overlap, competition coefficient, diet niche similarity, and relative hybrid fitness. Users supply a lineage-pair dataset and a phylogeny. 'phylopairs' calculates a covariance matrix for the pairwise-defined data and provides built-in models to test for relationships among variables while taking this covariance into account. Bayesian sampling is run through built-in 'Stan' programs via the 'rstan' package. The various models and methods that this package makes available are described in Anderson et al. (In Review), Coyne and Orr (1989) <doi:10.1111/j.1558-5646.1989.tb04233.x>, Fitzpatrick (2002) <doi:10.1111/j.0014-3820.2002.tb00860.x>, and Castillo (2007) <doi:10.1002/ece3.3093>.

Version: 0.1.0
Depends: R (≥ 3.5.0)
Imports: ape, loo, methods, phytools, Rcpp (≥ 0.12.0), RcppParallel (≥ 5.0.1), rstan (≥ 2.18.1), rstantools (≥ 2.4.0)
LinkingTo: BH (≥ 1.66.0), Rcpp (≥ 0.12.0), RcppEigen (≥ 0.3.3.3.0), RcppParallel (≥ 5.0.1), rstan (≥ 2.18.1), StanHeaders (≥ 2.18.0)
Published: 2024-06-25
DOI: 10.32614/CRAN.package.phylopairs
Author: Sean A. S. Anderson [aut, cre]
Maintainer: Sean A. S. Anderson <sean.as.anderson at gmail.com>
License: GPL (≥ 3)
NeedsCompilation: yes
SystemRequirements: GNU make
CRAN checks: phylopairs results

Documentation:

Reference manual: phylopairs.pdf

Downloads:

Package source: phylopairs_0.1.0.tar.gz
Windows binaries: r-devel: phylopairs_0.1.0.zip, r-release: phylopairs_0.1.0.zip, r-oldrel: phylopairs_0.1.0.zip
macOS binaries: r-release (arm64): phylopairs_0.1.0.tgz, r-oldrel (arm64): phylopairs_0.1.0.tgz, r-release (x86_64): phylopairs_0.1.0.tgz, r-oldrel (x86_64): phylopairs_0.1.0.tgz

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.