cauphy: Trait Evolution on Phylogenies Using the Cauchy Process

The Cauchy Process can model pulsed continuous trait evolution on phylogenies. The likelihood is tractable, and is used for parameter inference and ancestral trait reconstruction. See Bastide and Didier (2023) <doi:10.1093/sysbio/syad053>.

Version: 1.0.2
Depends: R (≥ 3.5), ape (≥ 5.5)
Imports: methods, robustbase, phylolm, nloptr, pracma, foreach, doParallel, HDInterval
Suggests: covr, knitr, rmarkdown, spelling, geiger, testthat (≥ 3.0.0)
Published: 2023-11-29
Author: Gilles Didier [aut, cph], Paul Bastide [aut, cre]
Maintainer: Paul Bastide <paul.bastide at cnrs.fr>
BugReports: https://github.com/gilles-didier/cauphy/issues
License: GPL (≥ 3)
URL: https://gilles-didier.github.io/cauphy/
NeedsCompilation: yes
Language: en-US
Citation: cauphy citation info
Materials: README NEWS
CRAN checks: cauphy results

Documentation:

Reference manual: cauphy.pdf
Vignettes: Example Analysis

Downloads:

Package source: cauphy_1.0.2.tar.gz
Windows binaries: r-devel: cauphy_1.0.2.zip, r-release: cauphy_1.0.2.zip, r-oldrel: cauphy_1.0.2.zip
macOS binaries: r-release (arm64): cauphy_1.0.2.tgz, r-oldrel (arm64): cauphy_1.0.2.tgz, r-release (x86_64): cauphy_1.0.2.tgz
Old sources: cauphy archive

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