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")

1.9.1 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]


Documentation:   PDF Manual  


Task views:


GPL (>= 2) license


Imports parallel, phytools, data.table, methods, diversitree, plotrix

Depends on ape, deSolve, GenSA, subplex, nloptr

Suggests testthat, knitr


Suggested by fishtree.


See at CRAN