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.


Windows users install Rtools first.



Reference manual

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1.8.5 by Jeremy Beaulieu, a month ago

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

Authors: Jeremy Beaulieu [aut, cre], Brian O'Meara [aut]

Documentation:   PDF Manual  

GPL (>= 2) license

Imports parallel, phytools, data.table, methods

Depends on ape, deSolve, GenSA, subplex, nloptr

Suggests testthat, diversitree, knitr

See at CRAN