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hisse: Hidden State Speciation and Extinction

Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification. Beaulieu and O'Meara (2016) <doi:10.1093/sysbio/syw022>.

Version: 2.1.11
Depends: ape, deSolve, GenSA, subplex, nloptr
Imports: parallel, phytools, data.table, igraph, methods, diversitree, paleotree, plotrix, geiger, phangorn, TreeSim, corHMM
Suggests: testthat, knitr, rmarkdown, markdown
Published: 2023-02-11
DOI: 10.32614/CRAN.package.hisse
Author: Jeremy Beaulieu [aut, cre], Brian O'Meara [aut], Daniel Caetano [aut], James Boyko [aut], Thais Vasconcelos [aut]
Maintainer: Jeremy Beaulieu <jmbeauli at uark.edu>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
Citation: hisse citation info
In views: Phylogenetics
CRAN checks: hisse results

Documentation:

Reference manual: hisse.pdf
Vignettes: The Problem with Clade-specific Sampling Fractions
Running GeoHiSSE
Running MiSSE
Running MuHiSSE
Incorporating Fossils in HiSSE, MuHiSSE, and MiSSE
Type I errors, Model rejection, & HiSSE vs. FiSSE
A newer, faster HiSSE function
Running the old HiSSE function

Downloads:

Package source: hisse_2.1.11.tar.gz
Windows binaries: r-devel: hisse_2.1.11.zip, r-release: hisse_2.1.11.zip, r-oldrel: hisse_2.1.11.zip
macOS binaries: r-release (arm64): hisse_2.1.11.tgz, r-oldrel (arm64): hisse_2.1.11.tgz, r-release (x86_64): hisse_2.1.11.tgz, r-oldrel (x86_64): hisse_2.1.11.tgz
Old sources: hisse archive

Reverse dependencies:

Reverse suggests: fishtree

Linking:

Please use the canonical form https://CRAN.R-project.org/package=hisse to link to this page.

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.