├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ └── pkgdown.yaml ├── .gitignore ├── ChangeLog ├── DESCRIPTION ├── Makefile ├── NAMESPACE ├── R ├── asr-bisse.R ├── asr-geosse.R ├── asr-mkn.R ├── asr-musse.R ├── asr-t.R ├── asr.R ├── check.R ├── clade-tree.R ├── constrain.R ├── continuous.R ├── desolve.R ├── diversitree-branches.R ├── drop.tip.fixed.R ├── dtlik.R ├── expm.R ├── gslode.R ├── history.R ├── mcmc-hmc.R ├── mcmc-norm.R ├── mcmc-slice.R ├── mcmc.R ├── mle-grid.R ├── mle-integer.R ├── mle-methods.R ├── mle-mixed.R ├── mle-optimize.R ├── mle-subplexR.R ├── mle.R ├── model-bd-nee.R ├── model-bd-ode.R ├── model-bd-split.R ├── model-bd-t.R ├── model-bd.R ├── model-bisse-split.R ├── model-bisse-t.R ├── model-bisse-td.R ├── model-bisse-unresolved.R ├── model-bisse.R ├── model-bisseness-unresolved.R ├── model-bisseness.R ├── model-bm-contrasts.R ├── model-bm-pruning.R ├── model-bm-vcv.R ├── model-bm.R ├── model-classe.R ├── model-eb.R ├── model-geosse-split.R ├── model-geosse-t.R ├── model-geosse.R ├── model-lambda.R ├── model-mkn-meristic.R ├── model-mkn-multitrait.R ├── model-mkn-ode.R ├── model-mkn-pij.R ├── model-mkn.R ├── model-musse-multitrait.R ├── model-musse-split.R ├── model-musse-t.R ├── model-musse-td.R ├── model-musse.R ├── model-ou-pruning.R ├── model-ou.R ├── model-pgls.R ├── model-quasse-common.R ├── model-quasse-fftC.R ├── model-quasse-fftR.R ├── model-quasse-mol.R ├── model-quasse-split.R ├── model-quasse.R ├── plot-alt-extra.R ├── plot-alt-util.R ├── plot-alt.R ├── profiles-plot.R ├── rescale.R ├── sim-character.R ├── simulate-bd.R ├── simulate-bisse.R ├── simulate-bisseness.R ├── simulate-classe.R ├── simulate-geosse.R ├── simulate-musse.R ├── simulate-quasse.R ├── simulation.R ├── split.R ├── t.R ├── td.R ├── time-machine.R ├── util-tree.R ├── util.R └── zzz.R ├── README.md ├── TODO ├── cleanup ├── configure ├── configure.ac ├── configure.win ├── doc ├── .interactive ├── Makefile ├── data │ ├── Lislevand-states.csv │ ├── Redding-2010.csv │ ├── Thomas-tree-exemplar.nex │ ├── Thomas-tree.nex │ ├── Thomas-unresolved.csv │ ├── Vos-2006.nex │ ├── arc.dat │ ├── arc.tre │ ├── cea.dat │ ├── cea.tre │ └── shorebird-families.csv ├── derivations.tex ├── diversitree-ext-bisse.c ├── diversitree-ext-cvodes.c ├── diversitree-ext-mk2.c ├── diversitree-ext.Rnw ├── diversitree-tutorial.Rnw ├── dtsweave.sty ├── refs.bib └── refstyle.bst ├── inst ├── CITATION ├── CONTRIBUTORS.md ├── tests │ ├── bisse-tree.ttn │ ├── classe-tree.ttn │ ├── geosse-tree.ttn │ ├── helper-diversitree.R │ ├── phy.Rdata │ ├── run-tests.R │ ├── test-asr-t.R │ ├── test-asr.R │ ├── test-bd-split.R │ ├── test-bd-t.R │ ├── test-bd.R │ ├── test-bisse-split.R │ ├── test-bisse-t.R │ ├── test-bisse-td.R │ ├── test-bisse.R │ ├── test-bisseness.R │ ├── test-bm.R │ ├── test-branches.R │ ├── test-classe.R │ ├── test-eb.R │ ├── test-geosse-t.R │ ├── test-geosse.R │ ├── test-lambda.R │ ├── test-mcmc.R │ ├── test-mkn.R │ ├── test-mle.R │ ├── test-musse-multitrait.R │ ├── test-musse-split.R │ ├── test-musse-t.R │ ├── test-musse.R │ ├── test-ode.R │ ├── test-ou.R │ ├── test-pgls.R │ ├── test-quasse-internal.R │ ├── test-quasse-split.R │ ├── test-quasse.R │ ├── test-rescale.R │ ├── test-time-machine.R │ ├── test-unresolved.R │ └── test-utils.R └── update-gh-pages.sh ├── man ├── argnames.Rd ├── asr-bisse.Rd ├── asr-mkn.Rd ├── asr.Rd ├── big.brother.Rd ├── check.Rd ├── combine.Rd ├── constants.Rd ├── constrain.Rd ├── diversitree-deprecated.Rd ├── diversitree-package.Rd ├── find.mle.Rd ├── history.from.sim.Rd ├── make.bd.Rd ├── make.bd.split.Rd ├── make.bd.t.Rd ├── make.bisse.Rd ├── make.bisse.split.Rd ├── make.bisse.td.Rd ├── make.bisseness.Rd ├── make.bm.Rd ├── make.clade.tree.Rd ├── make.classe.Rd ├── make.geosse.Rd ├── make.geosse.split.Rd ├── make.geosse.t.Rd ├── make.mkn.Rd ├── make.musse.Rd ├── make.musse.multitrait.Rd ├── make.musse.split.Rd ├── make.musse.td.Rd ├── make.pgls.Rd ├── make.prior.Rd ├── make.quasse.Rd ├── make.quasse.split.Rd ├── mcmc.Rd ├── plot.history.Rd ├── profiles.plot.Rd ├── protect.Rd ├── quasse-common.Rd ├── set.defaults.Rd ├── sim.character.Rd ├── simulate.Rd ├── trait.plot.Rd └── utils.Rd ├── pub ├── Makefile ├── bm │ ├── bm-timing-fun.R │ └── bm-timing.R ├── diversitree-suppl.tex ├── diversitree.tex ├── dtsweave.sty ├── example │ ├── .interactive │ ├── Makefile │ ├── data │ │ ├── primates-100.nex │ │ └── primates-social.csv │ ├── dtsweave.sty │ ├── primates.Rnw │ └── refstyle.bst ├── jecol.bst ├── ms.sty ├── refs.bib ├── simulations │ ├── musse-simulations-fun.R │ └── musse-simulations.R └── suppmat.sty ├── push-www.sh ├── run_tests.R ├── src ├── GNUmakefile ├── GslOdeBase.cpp ├── GslOdeBase.h ├── GslOdeCompiled.cpp ├── GslOdeCompiled.h ├── GslOdeR.cpp ├── GslOdeR.h ├── GslOdeTime.cpp ├── GslOdeTime.h ├── Makevars.in ├── Makevars.win ├── Spline.cpp ├── Spline.h ├── TimeMachine.cpp ├── TimeMachine.h ├── asr-joint.c ├── bd-eqs.c ├── bisse-eqs.c ├── bisseness-eqs.c ├── classe-eqs.c ├── config.h.in ├── config.h.win ├── continuous.c ├── continuous.h ├── derivs.c ├── derivs.h ├── geosse-eqs.c ├── hdr.c ├── hdr.h ├── interface.cpp ├── mkn-eqs.c ├── mkn-meristic-eqs.c ├── mkn-pij.c ├── mkn-pij.h ├── musse-eqs.c ├── quasse-eqs-fftC.c ├── quasse-eqs-fftC.h ├── quasse-eqs-mol.c ├── rfftw.c ├── rfftw.h ├── scm-mkn.c ├── scm-mkn.h ├── simulate-bisse.c ├── util-matrix.c ├── util-matrix.h ├── util-splines.c ├── util-splines.h ├── util.c ├── util.h ├── zzz.c └── zzz.h └── www ├── Makevars ├── archive ├── diversitree-bisse_0.2-1.pdf ├── diversitree-bisse_0.3-2.pdf ├── diversitree-tutorial-0.5_3.pdf ├── diversitree_0.2-1.tar.gz ├── diversitree_0.3-1.tar.gz ├── diversitree_0.3-2.tar.gz ├── diversitree_0.4-1.tar.gz ├── diversitree_0.4-2.tar.gz ├── diversitree_0.4-3.tar.gz ├── diversitree_0.4-4.tar.gz ├── diversitree_0.4-5.tar.gz ├── diversitree_0.5-2.tar.gz ├── diversitree_0.5-3.tar.gz ├── diversitree_0.6-1.tar.gz ├── diversitree_0.6-3.tar.gz ├── 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