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


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


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


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