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/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/muhisse.R R/plotContMapHiSSE.R R/plotHisse.R R/simulateGeoHiSSE.R R/simulateHisse.R R/singleModels.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/transMat.old.R R/transMatGeoHiSSE.R R/transMatGeoHiSSE.old.R R/transMatHiSSE.R R/transMatMuHiSSE.R README.md
docs/404.html
docs/articles/Clade-specific-sampling.html
docs/articles/Clade-specific-sampling_files/header-attrs-2.6/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-2.6/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-2.6/header-attrs.js
docs/articles/MuHiSSE-vignette.html
docs/articles/MuHiSSE-vignette_files/header-attrs-2.6/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-2.6/header-attrs.js
docs/articles/hisse-new-vignette.html
docs/articles/hisse-new-vignette_files/header-attrs-2.6/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-2.6/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/GeoHiSSE.html
docs/reference/GeoHiSSE.old.html
docs/reference/GetAICWeights.html
docs/reference/MiSSE.html
docs/reference/MiSSEGreedy.html
docs/reference/MuHiSSE.html
docs/reference/Rplot001.png
docs/reference/SimulateGeoHiSSE.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
inst/CITATION
inst/extdata/conifers_reconlist.rda
man/GeoHiSSE.Rd man/GeoHiSSE.old.Rd man/GetAICWeights.Rd man/MiSSE.Rd man/MiSSEGreedy.Rd man/MuHiSSE.Rd man/PruneRedundantModels.Rd man/SimulateGeoHiSSE.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/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.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/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
thej022214/hisse documentation built on May 15, 2021, 9:23 a.m.