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Hidden State Speciation and Extinction

Installation

About

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.

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Key Metrics

Version 2.1.10
Published 2023-01-19 463 days ago
Needs compilation? yes
License GPL-2
License GPL-3
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Maintainer

Maintainer

Jeremy Beaulieu

jmbeauli@uark.edu

Authors

Jeremy Beaulieu

aut / cre

Brian O'Meara

aut

Daniel Caetano

aut

James Boyko

aut

Thais Vasconcelos

aut

Material

Reference manual
Package source

In Views

Phylogenetics

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

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

hisse archive

Depends

ape
deSolve
GenSA
subplex
nloptr

Imports

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

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knitr
rmarkdown
markdown

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