hisse: Hidden State Speciation and Extinction
Version 1.8.2

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.

Browse man pages Browse package API and functions Browse package files

AuthorJeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>
Date of publication2017-04-04 22:39:14 UTC
MaintainerJeremy Beaulieu <jbeaulieu@nimbios.org>
LicenseGPL (>= 2)
Version1.8.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("hisse")

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

Functions

AdaptiveConfidenceIntervalSampling Source code
BisseToHisse Man page Source code
CheckFull Source code
CheckKeepRunning Source code
ConvertManyToBinaryState Source code
ConvertManyToRate Source code
ConvertToBinaryState Source code
ConvertToRate Source code
DevOptimize Source code
DevOptimizeNull Source code
DownPass Source code
DownPassNull Source code
GenerateValues Source code
GetAICWeights Source code
GetAllModels.anc Source code
GetBirthRate Source code
GetConversionOfAncestralNode Source code
GetDeathRate Source code
GetNormalizedDensityPlot Source code
GetRateRange Source code
GetRelevantRowEntries Source code
MarginRecon Man page Source code
Multiply Source code
ParDrop Man page Source code
ParEqual Man page Source code
ParameterTransform Source code
ParametersToPass Source code
ParametersToPassNull Source code
PassAscertainmentFilter Source code
SimToPhylo Man page Source code
SimulateHisse Man page Source code
SupportRegion Man page Source code
TransMatMaker Man page Source code
contMapGivenAnc Source code
getState Source code
hisse Man page Source code
hisse.null4 Man page Source code
makeMappedEdge Source code
plot.hisse.states Man page Source code
print.hisse.fit Source code
print.hisse.null4.fit Source code
print.hisse.states Source code
print.hisse.support Source code
starting.point.generator Source code Source code
starting.point.tree Source code Source code

Files

inst
inst/doc
inst/doc/hisse-vignette.R
inst/doc/hisse-vignette.Rmd
inst/doc/hisse-vignette.html
tests
tests/testthat.R
tests/testthat
tests/testthat/test_simulator.R
tests/testthat/test_likelihood.R
src
src/bisse-ext-derivs.c
src/registerDynamicSymbol.c
src/hisse-ext-derivs.c
src/Makevars.in
src/hissenull-ext-derivs.c
src/Makevars.win
NAMESPACE
R
R/hisseNull4.R
R/bisse2hisse.R
R/hisse.R
R/transMat.R
R/marginRecon.R
R/simulateHisse.R
R/plotHisse.R
R/supportRegion.R
R/singleModels.R
vignettes
vignettes/testrecon1.Rsave
vignettes/hisse-vignette.Rmd
vignettes/testrecon2.Rsave
vignettes/testrecon3.Rsave
MD5
build
build/vignette.rds
DESCRIPTION
man
man/transMat.Rd
man/simToPhylo.Rd
man/simulateHisse.Rd
man/plotHisse.Rd
man/hisseNull4.Rd
man/marginRecon.Rd
man/bisse2hisse.Rd
man/supportRegion.Rd
man/hisse.Rd
hisse documentation built on May 19, 2017, 9:15 a.m.