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

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:

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