hisse: Hidden State Speciation and Extinction

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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.

Author
Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>
Date of publication
2016-08-25 10:00:53
Maintainer
Jeremy Beaulieu <jbeaulieu@nimbios.org>
License
GPL (>= 2)
Version
1.8

View on CRAN

Man pages

bisse2hisse
BisseToHisse
hisse
Hidden State Speciation and Extinction
hisseNull4
Four state trait-independent Hidden State Speciation and...
marginRecon
Ancestral State Estimation based on Marginal Reconstruction
plotHisse
Plotting function hisse.states objects
simToPhylo
Convert simulated result to a tree
simulateHisse
Simulate under a HiSSE model
supportRegion
Adaptive Sampling of the Likelihood Surface
transMat
Transition Rate matrix generator

Files in this package

hisse
hisse/inst
hisse/inst/doc
hisse/inst/doc/hisse-vignette.R
hisse/inst/doc/hisse-vignette.Rmd
hisse/inst/doc/hisse-vignette.html
hisse/tests
hisse/tests/testthat.R
hisse/tests/testthat
hisse/tests/testthat/test_simulator.R
hisse/tests/testthat/test_likelihood.R
hisse/src
hisse/src/bisse-ext-derivs.c
hisse/src/hisse-ext-derivs.c
hisse/src/Makevars.in
hisse/src/hissenull-ext-derivs.c
hisse/src/Makevars.win
hisse/NAMESPACE
hisse/R
hisse/R/hisseNull4.R
hisse/R/bisse2hisse.R
hisse/R/hisse.R
hisse/R/transMat.R
hisse/R/marginRecon.R
hisse/R/simulateHisse.R
hisse/R/plotHisse.R
hisse/R/supportRegion.R
hisse/R/singleModels.R
hisse/vignettes
hisse/vignettes/testrecon1.Rsave
hisse/vignettes/hisse-vignette.Rmd
hisse/vignettes/testrecon2.Rsave
hisse/vignettes/testrecon3.Rsave
hisse/README.md
hisse/MD5
hisse/build
hisse/build/vignette.rds
hisse/DESCRIPTION
hisse/man
hisse/man/transMat.Rd
hisse/man/simToPhylo.Rd
hisse/man/simulateHisse.Rd
hisse/man/plotHisse.Rd
hisse/man/hisseNull4.Rd
hisse/man/marginRecon.Rd
hisse/man/bisse2hisse.Rd
hisse/man/supportRegion.Rd
hisse/man/hisse.Rd