Files in richfitz/diversitree
Comparative 'Phylogenetic' Analyses of Diversification

.Rbuildignore
.gitignore
.travis.yml
ChangeLog
DESCRIPTION
Makefile
NAMESPACE
R/asr-bisse.R R/asr-geosse.R R/asr-mkn.R R/asr-musse.R R/asr-t.R R/asr.R R/check.R R/clade-tree.R R/constrain.R R/continuous.R R/desolve.R R/diversitree-branches.R R/drop.tip.fixed.R R/dtlik.R R/expm.R R/gslode.R R/history.R R/mcmc-hmc.R R/mcmc-norm.R R/mcmc-slice.R R/mcmc.R R/mle-grid.R R/mle-integer.R R/mle-methods.R R/mle-mixed.R R/mle-optimize.R R/mle-subplexR.R R/mle.R R/model-bd-nee.R R/model-bd-ode.R R/model-bd-split.R R/model-bd-t.R R/model-bd.R R/model-bisse-split.R R/model-bisse-t.R R/model-bisse-td.R R/model-bisse-unresolved.R R/model-bisse.R R/model-bisseness-unresolved.R R/model-bisseness.R R/model-bm-contrasts.R R/model-bm-pruning.R R/model-bm-vcv.R R/model-bm.R R/model-classe.R R/model-eb.R R/model-geosse-split.R R/model-geosse-t.R R/model-geosse.R R/model-lambda.R R/model-mkn-expokit.R R/model-mkn-meristic.R R/model-mkn-multitrait.R R/model-mkn-ode.R R/model-mkn-pij.R R/model-mkn.R R/model-musse-multitrait.R R/model-musse-split.R R/model-musse-t.R R/model-musse-td.R R/model-musse.R R/model-ou-pruning.R R/model-ou.R R/model-pgls.R R/model-quasse-common.R R/model-quasse-fftC.R R/model-quasse-fftR.R R/model-quasse-mol.R R/model-quasse-split.R R/model-quasse.R R/plot-alt-extra.R R/plot-alt-util.R R/plot-alt.R R/profiles-plot.R R/rescale.R R/sim-character.R R/simulate-bd.R R/simulate-bisse.R R/simulate-bisseness.R R/simulate-classe.R R/simulate-geosse.R R/simulate-musse.R R/simulate-quasse.R R/simulation.R R/split.R R/t.R R/td.R R/time-machine.R R/util-tree.R R/util.R R/zzz.R README.md
TODO
cleanup
configure
configure.ac
configure.win
doc/.interactive
doc/Makefile
doc/data/Lislevand-states.csv
doc/data/Redding-2010.csv
doc/data/Thomas-tree-exemplar.nex
doc/data/Thomas-tree.nex
doc/data/Thomas-unresolved.csv
doc/data/Vos-2006.nex
doc/data/arc.dat
doc/data/arc.tre
doc/data/cea.dat
doc/data/cea.tre
doc/data/shorebird-families.csv
doc/derivations.tex
doc/diversitree-ext-bisse.c
doc/diversitree-ext-cvodes.c
doc/diversitree-ext-mk2.c
doc/diversitree-ext.Rnw
doc/diversitree-tutorial.Rnw
doc/dtsweave.sty
doc/refs.bib
doc/refstyle.bst
inst/CITATION
inst/CONTRIBUTORS.md
inst/tests/bisse-tree.ttn
inst/tests/classe-tree.ttn
inst/tests/geosse-tree.ttn
inst/tests/helper-diversitree.R
inst/tests/phy.Rdata
inst/tests/run-tests.R inst/tests/test-asr-t.R inst/tests/test-asr.R inst/tests/test-bd-split.R inst/tests/test-bd-t.R inst/tests/test-bd.R inst/tests/test-bisse-split.R inst/tests/test-bisse-t.R inst/tests/test-bisse-td.R inst/tests/test-bisse.R inst/tests/test-bisseness.R inst/tests/test-bm.R inst/tests/test-branches.R inst/tests/test-classe.R inst/tests/test-eb.R inst/tests/test-expm.R inst/tests/test-geosse-t.R inst/tests/test-geosse.R inst/tests/test-lambda.R inst/tests/test-mcmc.R inst/tests/test-mkn.R inst/tests/test-mle.R inst/tests/test-musse-multitrait.R inst/tests/test-musse-split.R inst/tests/test-musse-t.R inst/tests/test-musse.R inst/tests/test-ode.R inst/tests/test-ou.R inst/tests/test-pgls.R inst/tests/test-quasse-internal.R inst/tests/test-quasse-split.R inst/tests/test-quasse.R inst/tests/test-rescale.R inst/tests/test-time-machine.R inst/tests/test-unresolved.R inst/tests/test-utils.R
inst/update-gh-pages.sh
man/argnames.Rd man/asr-bisse.Rd man/asr-mkn.Rd man/asr.Rd man/big.brother.Rd man/check.Rd man/combine.Rd man/constants.Rd man/constrain.Rd man/diversitree-deprecated.Rd man/diversitree-package.Rd man/find.mle.Rd man/geosse.phy.Rd man/history.from.sim.Rd man/make.bd.Rd man/make.bd.split.Rd man/make.bd.t.Rd man/make.bisse.Rd man/make.bisse.split.Rd man/make.bisse.td.Rd man/make.bisseness.Rd man/make.bm.Rd man/make.clade.tree.Rd man/make.classe.Rd man/make.geosse.Rd man/make.geosse.split.Rd man/make.geosse.t.Rd man/make.mkn.Rd man/make.musse.Rd man/make.musse.multitrait.Rd man/make.musse.split.Rd man/make.musse.td.Rd man/make.pgls.Rd man/make.prior.Rd man/make.quasse.Rd man/make.quasse.split.Rd man/mcmc.Rd man/plot.history.Rd man/profiles.plot.Rd man/protect.Rd man/quasse-common.Rd man/set.defaults.Rd man/sim.character.Rd man/simulate.Rd man/trait.plot.Rd man/utils.Rd
pub/Makefile
pub/bm/bm-timing-fun.R pub/bm/bm-timing.R
pub/diversitree-suppl.tex
pub/diversitree.tex
pub/dtsweave.sty
pub/example/.interactive
pub/example/Makefile
pub/example/data/primates-100.nex
pub/example/data/primates-social.csv
pub/example/dtsweave.sty
pub/example/primates.Rnw
pub/example/refstyle.bst
pub/jecol.bst
pub/ms.sty
pub/refs.bib
pub/simulations/musse-simulations-fun.R pub/simulations/musse-simulations.R
pub/suppmat.sty
push-www.sh
run_tests.R
src/GNUmakefile
src/GslOdeBase.cpp
src/GslOdeBase.h
src/GslOdeCompiled.cpp
src/GslOdeCompiled.h
src/GslOdeR.cpp
src/GslOdeR.h
src/GslOdeTime.cpp
src/GslOdeTime.h
src/Makevars.in
src/Makevars.win
src/Spline.cpp
src/Spline.h
src/TimeMachine.cpp
src/TimeMachine.h
src/asr-joint.c
src/bd-eqs.c
src/bisse-eqs.c
src/bisseness-eqs.c
src/bucexp.f
src/classe-eqs.c
src/config.h.in
src/config.h.win
src/continuous.c
src/continuous.h
src/derivs.c
src/derivs.h
src/dgcoov.f
src/dgexpvi.f
src/dgpadm.f
src/dmexpv.f
src/dnchbv.f
src/dsexpv.f
src/dsexpvi.f
src/expm.f
src/geosse-eqs.c
src/hdr.c
src/hdr.h
src/hyperg.f
src/interface.cpp
src/mkn-eqs.c
src/mkn-expokit.c
src/mkn-expokit.h
src/mkn-meristic-eqs.c
src/mkn-pij.c
src/mkn-pij.h
src/musse-eqs.c
src/nucexp.f
src/quasse-eqs-fftC.c
src/quasse-eqs-fftC.h
src/quasse-eqs-mol.c
src/rfftw.c
src/rfftw.h
src/scm-mkn.c
src/scm-mkn.h
src/simulate-bisse.c
src/util-matrix.c
src/util-matrix.h
src/util-splines.c
src/util-splines.h
src/util.c
src/util.h
src/zzz.c
src/zzz.h
www/Makevars
www/archive/diversitree-bisse_0.2-1.pdf www/archive/diversitree-bisse_0.3-2.pdf www/archive/diversitree-tutorial-0.5_3.pdf
www/archive/diversitree_0.2-1.tar.gz
www/archive/diversitree_0.3-1.tar.gz
www/archive/diversitree_0.3-2.tar.gz
www/archive/diversitree_0.4-1.tar.gz
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www/archive/diversitree_0.4-3.tar.gz
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www/archive/diversitree_0.6-1.tar.gz
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www/archive/diversitree_0.7-1.tar.gz
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www/archive/diversitree_0.7-6.tar.gz
www/archive/diversitree_0.7-7.tar.gz
www/archive/diversitree_0.7-7.zip
www/archive/diversitree_0.8-4.tar.gz
www/archive/diversitree_0.9-1.tar.gz
www/archive/diversitree_0.9-3.tar.gz
www/archive/medusa2_0.1-1.tar.gz
www/bib/Makefile
www/bib/process.py
www/bib/studies.bib
www/bib/stylesheet.css
www/bib/sysbio3.bst
www/bib/template.html
www/changes.html
www/doc/files/index.html
www/examples/clean-example.sh
www/examples/compile-example.sh
www/examples/index.html
www/examples/ou-nonultrametric/ou-nonultrametric.R
www/examples/refs.bib
www/examples/stylesheet.css
www/examples/uneven/uneven.R www/examples/unreplicated/unreplicated.R
www/faq.html
www/index.html
www/installation.html
www/logo/beetles.eps
www/logo/logo-on-black.R www/logo/logo.R
www/pics/logo.png
www/stylesheet.css
richfitz/diversitree documentation built on May 25, 2017, 2:11 a.m.