Files in thej022214/hisse
Hidden State Speciation and Extinction
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/FindGenerations.R
R/GenerateValues.R
R/GetModelWeight.R
R/PruneRedundantModels.R
R/fossilUtilities.R
R/geohisse.R
R/geohisse.old.R
R/geohisseLikelihood.R
R/getModelAveTipRates.R
R/hisse.R
R/hisse.old.R
R/hisseLikelihood.R
R/hisseNull4.old.R
R/marginRecon.R
R/misse.R
R/misseNet.R
R/muhisse.R
R/plotContMapHiSSE.R
R/plotHisse.R
R/simulateGeoHiSSE.R
R/simulateHisse.R
R/singleModels.R
R/startingPointGenerators.R
R/summarizeHisse.R
R/supportRegion.old.R
R/supportRegionGeoSSE.R
R/supportRegionGeoSSE.old.R
R/supportRegionHiSSE.R
R/supportRegionMiSSE.R
R/supportRegionMuHiSSE.R
R/tipCorrelation.R
R/transMat.old.R
R/transMatGeoHiSSE.R
R/transMatGeoHiSSE.old.R
R/transMatHiSSE.R
R/transMatMuHiSSE.R
README.md
docs/404.html
docs/CNAME
docs/articles/Clade-specific-sampling.html
docs/articles/Clade-specific-sampling_files/header-attrs-2.11.3/header-attrs.js
docs/articles/Clade-specific-sampling_files/header-attrs-2.6/header-attrs.js
docs/articles/Clade-specific-sampling_files/header-attrs-2.8/header-attrs.js
docs/articles/GeoHiSSE-vignette.html
docs/articles/GeoHiSSE-vignette_files/figure-html/fig1-1.png
docs/articles/GeoHiSSE-vignette_files/header-attrs-2.11.3/header-attrs.js
docs/articles/GeoHiSSE-vignette_files/header-attrs-2.6/header-attrs.js
docs/articles/GeoHiSSE-vignette_files/header-attrs-2.8/header-attrs.js
docs/articles/MiSSE-vignette.html
docs/articles/MiSSE-vignette_files/figure-html/unnamed-chunk-12-1.png
docs/articles/MiSSE-vignette_files/figure-html/unnamed-chunk-6-1.png
docs/articles/MiSSE-vignette_files/figure-html/unnamed-chunk-9-1.png
docs/articles/MiSSE-vignette_files/header-attrs-2.11.3/header-attrs.js
docs/articles/MiSSE-vignette_files/header-attrs-2.6/header-attrs.js
docs/articles/MiSSE-vignette_files/header-attrs-2.8/header-attrs.js
docs/articles/MuHiSSE-vignette.html
docs/articles/MuHiSSE-vignette_files/header-attrs-2.11.3/header-attrs.js
docs/articles/MuHiSSE-vignette_files/header-attrs-2.6/header-attrs.js
docs/articles/MuHiSSE-vignette_files/header-attrs-2.8/header-attrs.js
docs/articles/adding_fossils.html
docs/articles/adding_fossils_files/figure-html/unnamed-chunk-16-1.png
docs/articles/adding_fossils_files/figure-html/unnamed-chunk-17-1.png
docs/articles/adding_fossils_files/header-attrs-2.11.3/header-attrs.js
docs/articles/adding_fossils_files/header-attrs-2.8/header-attrs.js
docs/articles/hisse-fisse-type1-vignette.html
docs/articles/hisse-fisse-type1-vignette_files/figure-html/unnamed-chunk-2-1.png
docs/articles/hisse-fisse-type1-vignette_files/figure-html/unnamed-chunk-3-1.png
docs/articles/hisse-fisse-type1-vignette_files/figure-html/unnamed-chunk-4-1.png
docs/articles/hisse-fisse-type1-vignette_files/figure-html/unnamed-chunk-5-1.png
docs/articles/hisse-fisse-type1-vignette_files/header-attrs-2.11.3/header-attrs.js
docs/articles/hisse-fisse-type1-vignette_files/header-attrs-2.6/header-attrs.js
docs/articles/hisse-fisse-type1-vignette_files/header-attrs-2.8/header-attrs.js
docs/articles/hisse-new-vignette.html
docs/articles/hisse-new-vignette_files/header-attrs-2.11.3/header-attrs.js
docs/articles/hisse-new-vignette_files/header-attrs-2.6/header-attrs.js
docs/articles/hisse-new-vignette_files/header-attrs-2.8/header-attrs.js
docs/articles/hisse-vignette.html
docs/articles/hisse-vignette_files/figure-html/unnamed-chunk-23-1.png
docs/articles/hisse-vignette_files/figure-html/unnamed-chunk-24-1.png
docs/articles/hisse-vignette_files/figure-html/unnamed-chunk-27-1.png
docs/articles/hisse-vignette_files/header-attrs-2.11.3/header-attrs.js
docs/articles/hisse-vignette_files/header-attrs-2.6/header-attrs.js
docs/articles/hisse-vignette_files/header-attrs-2.8/header-attrs.js
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/AddFossilPoints.html
docs/reference/AddStratIntervals.html
docs/reference/GeoHiSSE.html
docs/reference/GeoHiSSE.old.html
docs/reference/GetAICWeights.html
docs/reference/GetFossils.html
docs/reference/MiSSE.html
docs/reference/MiSSEGreedy.html
docs/reference/MiSSENet.html
docs/reference/MuHiSSE.html
docs/reference/PlotMisseSpace.html
docs/reference/ProcessSimSample.html
docs/reference/ProcessSimStrat.html
docs/reference/PruneRedundantModels.html
docs/reference/Rplot001.png
docs/reference/SimulateGeoHiSSE.html
docs/reference/SummarizeMiSSEGreedy.html
docs/reference/TipCorrelation.html
docs/reference/TranslateParsMakerGeoHiSSE.html
docs/reference/generateMiSSEGreedyCombinations.html
docs/reference/hisse.html
docs/reference/hisse.old.html
docs/reference/hisseNull4.old.html
docs/reference/index.html
docs/reference/makeGeoHiSSELikelihood.html
docs/reference/makeHiSSELikelihood.html
docs/reference/marginRecon.old.html
docs/reference/marginReconGeoSSE.html
docs/reference/marginReconGeoSSE.old.html
docs/reference/marginReconHiSSE.html
docs/reference/marginReconMiSSE.html
docs/reference/marginReconMuHiSSE.html
docs/reference/modelAveRates.html
docs/reference/plotGeoHiSSE.html
docs/reference/plotHisse.html
docs/reference/plotMiSSE.html
docs/reference/plotMuHiSSE.html
docs/reference/simToPhylo-1.png
docs/reference/simToPhylo.html
docs/reference/simulateHisse-1.png
docs/reference/simulateHisse.html
docs/reference/supportRegion.old.html
docs/reference/supportRegionGeoSSE.html
docs/reference/supportRegionGeoSSE.old.html
docs/reference/supportRegionHiSSE.html
docs/reference/supportRegionMiSSE.html
docs/reference/supportRegionMuHiSSE.html
docs/reference/transMat.html
docs/reference/transMatMakerGeoHiSSE.html
docs/reference/transMatMakerHiSSE.html
docs/reference/transMatMakerMuHiSSE.html
docs/sitemap.xml
inst/CITATION
man/AddFossilPoints.Rd
man/AddStratIntervals.Rd
man/GeoHiSSE.Rd
man/GeoHiSSE.old.Rd
man/GetAICWeights.Rd
man/GetFossils.Rd
man/MiSSE.Rd
man/MiSSEGreedy.Rd
man/MiSSENet.Rd
man/MuHiSSE.Rd
man/PlotMisseSpace.Rd
man/ProcessSimSample.Rd
man/ProcessSimStrat.Rd
man/PruneRedundantModels.Rd
man/SimulateGeoHiSSE.Rd
man/SummarizeMiSSEGreedy.Rd
man/TipCorrelation.Rd
man/TranslateParsMakerGeoHiSSE.Rd
man/generateMiSSEGreedyCombinations.Rd
man/hisse.Rd
man/hisse.old.Rd
man/hisseNull4.old.Rd
man/makeGeoHiSSELikelihood.Rd
man/makeHiSSELikelihood.Rd
man/marginRecon.old.Rd
man/marginReconGeoSSE.Rd
man/marginReconGeoSSE.old.Rd
man/marginReconHiSSE.Rd
man/marginReconMiSSE.Rd
man/marginReconMuHiSSE.Rd
man/modelAveRates.Rd
man/plotGeoHiSSE.Rd
man/plotHisse.Rd
man/plotMiSSE.Rd
man/plotMuHiSSE.Rd
man/simToPhylo.Rd
man/simulateHisse.Rd
man/supportRegion.old.Rd
man/supportRegionGeoSSE.Rd
man/supportRegionGeoSSE.old.Rd
man/supportRegionHiSSE.Rd
man/supportRegionMiSSE.Rd
man/supportRegionMuHiSSE.Rd
man/transMat.Rd
man/transMatMakerGeoHiSSE.Rd
man/transMatMakerHiSSE.Rd
man/transMatMakerMuHiSSE.Rd
src/Makevars
src/bisse-ext-derivs.c
src/canonical-musse-ext-derivs.c
src/canonical_geosse-ext-derivs.c
src/fbisse-ext-derivs.c
src/fcanonical_geosse-ext-derivs.c
src/fgeohisse-ext-derivs.c
src/fhisse-ext-derivs.c
src/fnotclasse-ext-derivs.c
src/fnotclasse-more-ext-derivs.c
src/geohisse-ext-derivs.c
src/hisse-ext-derivs.c
src/hissenull-ext-derivs.c
src/misse-ext-derivs.c
src/muhisse-ext-derivs.c
src/notclasse-ext-derivs.c
src/notclasse-more-ext-derivs.c
src/registerDynamicSymbol.c
tests/testthat.R
tests/testthat/CID2_MiSSE_check.Rsave
tests/testthat/test_likelihood.R
tests/testthat/test_simulator.R
tests/testthat/whales_Steemanetal2009.tre
vignettes/Clade-specific-sampling.Rmd
vignettes/Clade-specific-sampling.pdf
vignettes/GeoHiSSE-vignette.R
vignettes/GeoHiSSE-vignette.Rmd
vignettes/GeoHiSSE-vignette.pdf
vignettes/May2017_CID4_added_setsummaries.csv
vignettes/MiSSE-vignette.Rmd
vignettes/MiSSE-vignette.pdf
vignettes/MuHiSSE-vignette.Rmd
vignettes/MuHiSSE-vignette.pdf
vignettes/adding_fossils.Rmd
vignettes/adding_fossils.pdf
vignettes/cladeSamplingVariables.Rsave
vignettes/geohisse_new_vignette.Rsave
vignettes/geohisse_recons_new_vignette.Rsave
vignettes/geohisse_recons_vignette.Rsave
vignettes/geohisse_vignette.Rsave
vignettes/hisse-fisse-type1-vignette.Rmd
vignettes/hisse-fisse-type1-vignette.pdf
vignettes/hisse-new-vignette.Rmd
vignettes/hisse-new-vignette.pdf
vignettes/hisse-vignette.Rmd
vignettes/hisse-vignette.pdf
vignettes/misse.support.Rsave
vignettes/misse.vignette.Rsave
vignettes/setCAQTipRatios.Rsave
vignettes/setKXHTipRatios.Rsave
vignettes/setMEVTipRatios.Rsave
vignettes/testrecon1.Rsave
vignettes/testrecon2.Rsave
vignettes/testrecon3.Rsave
vignettes/whales_Steemanetal2009.tre
