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) .


hisse is currently in review; see the manuscript here.

install.packages("hisse")

Windows users install Rtools first.

install.packages("devtools")
devtools::install_github("thej022214/hisse")
library('hisse')

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Reference manual

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install.packages("hisse")

2.1.6 by Jeremy Beaulieu, 2 months ago


Browse source code at https://github.com/cran/hisse


Authors: Jeremy Beaulieu [aut, cre] , Brian O'Meara [aut] , Daniel Caetano [aut] , James Boyko [aut] , Thais Vasconcelos [aut]


Documentation:   PDF Manual  


Task views:


GPL (>= 2) license


Imports parallel, phytools, data.table, igraph, methods, diversitree, paleotree, plotrix, geiger, phangorn, TreeSim, corHMM

Depends on ape, deSolve, GenSA, subplex, nloptr

Suggests testthat, knitr, rmarkdown, markdown


Suggested by fishtree.


See at CRAN