├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── ChangeLog ├── DESCRIPTION ├── Makefile ├── NAMESPACE ├── R ├── TESTING.R ├── congruify.R ├── deprecated.R ├── disparity.R ├── diversification.R ├── diversitree.R ├── edges.R ├── examples.R ├── gbresolve.R ├── glomogram.R ├── internal.R ├── likelihood.R ├── mecca.R ├── medusa.R ├── plotting.R ├── postpred.R ├── proposals.R ├── rjmcmc.R ├── simulation.R ├── traits-fossil.R ├── traits.R ├── utilities-misc.R ├── utilities-phylo.R ├── utilities-print.R └── utilities-stat.R ├── README.md ├── data ├── amphibia.rda ├── caniformia.rda ├── carnivores.rda ├── caudata.rda ├── chelonia.rda ├── geospiza.rda ├── primates.rda └── whales.rda ├── geiger-v2.Rproj ├── inst └── CITATION ├── man ├── aicm.Rd ├── aicw.Rd ├── aov.phylo.Rd ├── bd.ms.Rd ├── calibrate.mecca.Rd ├── calibrate.rjmcmc.Rd ├── congruify.phylo.Rd ├── dcount.Rd ├── drop.extinct.Rd ├── dtt.Rd ├── fitContinuous.Rd ├── fitContinuousMCMC.Rd ├── fitDiscrete.Rd ├── gbresolve.Rd ├── geiger-data.Rd ├── geiger-defunct.Rd ├── geiger-examples.Rd ├── geiger-internal.Rd ├── geiger-package.Rd ├── load.rjmcmc.Rd ├── make.gbm.Rd ├── mecca.Rd ├── medusa.Rd ├── name.check.Rd ├── nh.test.Rd ├── nodelabel.phylo.Rd ├── plot.medusa.Rd ├── pp.mcmc.Rd ├── r8s.phylo.Rd ├── ratematrix.Rd ├── rc.Rd ├── rescale.phylo.Rd ├── rjmcmc.bm.Rd ├── sim.bd.Rd ├── sim.bdtree.Rd ├── sim.char.Rd ├── startingpt.mecca.Rd ├── subset.phylo.Rd ├── tips.Rd ├── to.auteur.Rd └── treedata.Rd ├── src-i386 ├── APE_reorder_phylo.c ├── Makevars ├── Makevars.win ├── branches.cpp ├── init.c ├── mkn.c ├── mkn.h ├── pic.c ├── symbols.rds ├── util.c ├── util.h └── utilities.cpp └── src ├── APE_reorder_phylo.c ├── Makevars ├── Makevars.win ├── branches.cpp ├── geiger.dll ├── init.c ├── mkn.c ├── mkn.h ├── pic.c ├── util.c ├── util.h └── utilities.cpp /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/.travis.yml -------------------------------------------------------------------------------- /ChangeLog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/ChangeLog -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/Makefile -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/TESTING.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/TESTING.R -------------------------------------------------------------------------------- /R/congruify.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/congruify.R -------------------------------------------------------------------------------- /R/deprecated.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/deprecated.R -------------------------------------------------------------------------------- /R/disparity.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/disparity.R -------------------------------------------------------------------------------- /R/diversification.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/diversification.R -------------------------------------------------------------------------------- /R/diversitree.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/diversitree.R -------------------------------------------------------------------------------- /R/edges.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/edges.R -------------------------------------------------------------------------------- /R/examples.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/examples.R -------------------------------------------------------------------------------- /R/gbresolve.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/gbresolve.R -------------------------------------------------------------------------------- /R/glomogram.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/glomogram.R -------------------------------------------------------------------------------- /R/internal.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/internal.R -------------------------------------------------------------------------------- /R/likelihood.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/likelihood.R -------------------------------------------------------------------------------- /R/mecca.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/mecca.R -------------------------------------------------------------------------------- /R/medusa.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/medusa.R -------------------------------------------------------------------------------- /R/plotting.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/plotting.R -------------------------------------------------------------------------------- /R/postpred.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/postpred.R -------------------------------------------------------------------------------- /R/proposals.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/proposals.R -------------------------------------------------------------------------------- /R/rjmcmc.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/rjmcmc.R -------------------------------------------------------------------------------- /R/simulation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/simulation.R -------------------------------------------------------------------------------- /R/traits-fossil.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/traits-fossil.R -------------------------------------------------------------------------------- /R/traits.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/traits.R -------------------------------------------------------------------------------- /R/utilities-misc.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/utilities-misc.R -------------------------------------------------------------------------------- /R/utilities-phylo.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/utilities-phylo.R -------------------------------------------------------------------------------- /R/utilities-print.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/utilities-print.R -------------------------------------------------------------------------------- /R/utilities-stat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/R/utilities-stat.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/README.md -------------------------------------------------------------------------------- /data/amphibia.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/data/amphibia.rda -------------------------------------------------------------------------------- /data/caniformia.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/data/caniformia.rda -------------------------------------------------------------------------------- /data/carnivores.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/data/carnivores.rda -------------------------------------------------------------------------------- /data/caudata.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/data/caudata.rda -------------------------------------------------------------------------------- /data/chelonia.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/data/chelonia.rda -------------------------------------------------------------------------------- /data/geospiza.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/data/geospiza.rda -------------------------------------------------------------------------------- /data/primates.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/data/primates.rda -------------------------------------------------------------------------------- /data/whales.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/data/whales.rda -------------------------------------------------------------------------------- /geiger-v2.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/geiger-v2.Rproj -------------------------------------------------------------------------------- /inst/CITATION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/inst/CITATION -------------------------------------------------------------------------------- /man/aicm.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/aicm.Rd -------------------------------------------------------------------------------- /man/aicw.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/aicw.Rd -------------------------------------------------------------------------------- /man/aov.phylo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/aov.phylo.Rd -------------------------------------------------------------------------------- /man/bd.ms.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/bd.ms.Rd -------------------------------------------------------------------------------- /man/calibrate.mecca.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/calibrate.mecca.Rd -------------------------------------------------------------------------------- /man/calibrate.rjmcmc.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/calibrate.rjmcmc.Rd -------------------------------------------------------------------------------- /man/congruify.phylo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/congruify.phylo.Rd -------------------------------------------------------------------------------- /man/dcount.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/dcount.Rd -------------------------------------------------------------------------------- /man/drop.extinct.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/drop.extinct.Rd -------------------------------------------------------------------------------- /man/dtt.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/dtt.Rd -------------------------------------------------------------------------------- /man/fitContinuous.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/fitContinuous.Rd -------------------------------------------------------------------------------- /man/fitContinuousMCMC.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/fitContinuousMCMC.Rd -------------------------------------------------------------------------------- /man/fitDiscrete.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/fitDiscrete.Rd -------------------------------------------------------------------------------- /man/gbresolve.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/gbresolve.Rd -------------------------------------------------------------------------------- /man/geiger-data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/geiger-data.Rd -------------------------------------------------------------------------------- /man/geiger-defunct.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/geiger-defunct.Rd -------------------------------------------------------------------------------- /man/geiger-examples.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/geiger-examples.Rd -------------------------------------------------------------------------------- /man/geiger-internal.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/geiger-internal.Rd -------------------------------------------------------------------------------- /man/geiger-package.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/geiger-package.Rd -------------------------------------------------------------------------------- /man/load.rjmcmc.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/load.rjmcmc.Rd -------------------------------------------------------------------------------- /man/make.gbm.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/make.gbm.Rd -------------------------------------------------------------------------------- /man/mecca.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/mecca.Rd -------------------------------------------------------------------------------- /man/medusa.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/medusa.Rd -------------------------------------------------------------------------------- /man/name.check.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/name.check.Rd -------------------------------------------------------------------------------- /man/nh.test.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/nh.test.Rd -------------------------------------------------------------------------------- /man/nodelabel.phylo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/nodelabel.phylo.Rd -------------------------------------------------------------------------------- /man/plot.medusa.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/plot.medusa.Rd -------------------------------------------------------------------------------- /man/pp.mcmc.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/pp.mcmc.Rd -------------------------------------------------------------------------------- /man/r8s.phylo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/r8s.phylo.Rd -------------------------------------------------------------------------------- /man/ratematrix.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/ratematrix.Rd -------------------------------------------------------------------------------- /man/rc.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/rc.Rd -------------------------------------------------------------------------------- /man/rescale.phylo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/rescale.phylo.Rd -------------------------------------------------------------------------------- /man/rjmcmc.bm.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/rjmcmc.bm.Rd -------------------------------------------------------------------------------- /man/sim.bd.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/sim.bd.Rd -------------------------------------------------------------------------------- /man/sim.bdtree.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/sim.bdtree.Rd -------------------------------------------------------------------------------- /man/sim.char.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/sim.char.Rd -------------------------------------------------------------------------------- /man/startingpt.mecca.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/startingpt.mecca.Rd -------------------------------------------------------------------------------- /man/subset.phylo.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/subset.phylo.Rd -------------------------------------------------------------------------------- /man/tips.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/tips.Rd -------------------------------------------------------------------------------- /man/to.auteur.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/to.auteur.Rd -------------------------------------------------------------------------------- /man/treedata.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/man/treedata.Rd -------------------------------------------------------------------------------- /src-i386/APE_reorder_phylo.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src-i386/APE_reorder_phylo.c -------------------------------------------------------------------------------- /src-i386/Makevars: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src-i386/Makevars -------------------------------------------------------------------------------- /src-i386/Makevars.win: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src-i386/Makevars.win -------------------------------------------------------------------------------- /src-i386/branches.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src-i386/branches.cpp -------------------------------------------------------------------------------- /src-i386/init.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src-i386/init.c -------------------------------------------------------------------------------- /src-i386/mkn.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src-i386/mkn.c -------------------------------------------------------------------------------- /src-i386/mkn.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src-i386/mkn.h -------------------------------------------------------------------------------- /src-i386/pic.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src-i386/pic.c -------------------------------------------------------------------------------- /src-i386/symbols.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src-i386/symbols.rds -------------------------------------------------------------------------------- /src-i386/util.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src-i386/util.c -------------------------------------------------------------------------------- /src-i386/util.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src-i386/util.h -------------------------------------------------------------------------------- /src-i386/utilities.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src-i386/utilities.cpp -------------------------------------------------------------------------------- /src/APE_reorder_phylo.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src/APE_reorder_phylo.c -------------------------------------------------------------------------------- /src/Makevars: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src/Makevars -------------------------------------------------------------------------------- /src/Makevars.win: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src/Makevars.win -------------------------------------------------------------------------------- /src/branches.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src/branches.cpp -------------------------------------------------------------------------------- /src/geiger.dll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src/geiger.dll -------------------------------------------------------------------------------- /src/init.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src/init.c -------------------------------------------------------------------------------- /src/mkn.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src/mkn.c -------------------------------------------------------------------------------- /src/mkn.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src/mkn.h -------------------------------------------------------------------------------- /src/pic.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src/pic.c -------------------------------------------------------------------------------- /src/util.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src/util.c -------------------------------------------------------------------------------- /src/util.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src/util.h -------------------------------------------------------------------------------- /src/utilities.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mwpennell/geiger-v2/HEAD/src/utilities.cpp --------------------------------------------------------------------------------