geiger: Analysis of Evolutionary Diversification

Share:

Methods for fitting macroevolutionary models to phylogenetic trees.

Author
Luke Harmon <lukeh@uidaho.edu>, Jason Weir, Chad Brock, Rich Glor, Wendell Challenger, Gene Hunt, Rich FitzJohn, Matt Pennell, Graham Slater, Joseph Brown, Josef Uyeda, and Jon Eastman <jonathan.eastman@gmail.com>
Date of publication
2015-09-07 21:26:42
Maintainer
Matt Pennell <mwpennell@gmail.com>
License
GPL (>= 2)
Version
2.0.6
URLs

View on CRAN

Man pages

aicm
Akaike's Information Criterion for MCMC samples (AICM)
aicw
determining Akaike weights
aov.phylo
phylogenetic ANOVA and MANOVA
bd.ms
estimate net diversification rate
calibrate.mecca
calibrating MECCA
calibrate.rjmcmc
initialize proposal width
congruify.phylo
ultrametricization of trees from a supplied timetree
dcount
prior densities for truncated discrete random variable
drop.extinct
prune specified taxa from a phylogenetic tree
dtt
disparity-through-time
fitContinuous
model fitting for continuous comparative data
fitContinuousMCMC
Fit models of continuous trait evolution to comparative data...
fitDiscrete
model fitting for discrete comparative data
gbresolve
NCBI taxonomy
geiger-data
example datasets
geiger-defunct
deprecated functions in GEIGER
geiger-examples
internal geiger functions
geiger-internal
internal geiger functions
geiger-package
GEIGER
load.rjmcmc
posterior samples from single or multiple MCMC runs
make.gbm
tailor reversible-jump Markov chain Monte Carlo sampling
mecca
running a MECCA analysis
medusa
MEDUSA: modeling evolutionary diversification using stepwise...
name.check
Compares taxa in data and tree
nh.test
using the Freckleton and Harvey node-height test
nodelabel.phylo
Blending information from taxonomies and trees
plot.medusa
MEDUSA: modeling evolutionary diversification using stepwise...
pp.mcmc
using posterior predictive MCMC for modeling quantitative...
ratematrix
evolutionary VCV matrix
rc
relative cladogenesis test
rescale
Tree transformations
rjmcmc.bm
Bayesian sampling of shifts in trait evolution: relaxed...
sim.bd
birth-death population simulator
sim.bdtree
birth-death tree simulator
sim.char
simulate character evolution
startingpt.mecca
starting values for MECCA
subset.phylo
blending information from taxonomies and trees
tips
descendents of a given node in a phylogenetic tree
to.auteur
conversion of MCMC samples between auteur and coda
treedata
compare taxa in data and tree

Files in this package

geiger
geiger/inst
geiger/inst/CITATION
geiger/src
geiger/src/Makevars
geiger/src/util.c
geiger/src/pic.c
geiger/src/APE_reorder_phylo.c
geiger/src/mkn.c
geiger/src/util.h
geiger/src/branches.cpp
geiger/src/Makevars.win
geiger/src/utilities.cpp
geiger/src/mkn.h
geiger/NAMESPACE
geiger/data
geiger/data/primates.rda
geiger/data/caniformia.rda
geiger/data/chelonia.rda
geiger/data/caudata.rda
geiger/data/carnivores.rda
geiger/data/amphibia.rda
geiger/data/whales.rda
geiger/data/geospiza.rda
geiger/R
geiger/R/diversification.R
geiger/R/plotting.R
geiger/R/postpred.R
geiger/R/glomogram.R
geiger/R/utilities-stat.R
geiger/R/gbresolve.R
geiger/R/congruify.R
geiger/R/rjmcmc.R
geiger/R/TESTING.R
geiger/R/simulation.R
geiger/R/traits.R
geiger/R/internal.R
geiger/R/deprecated.R
geiger/R/utilities-misc.R
geiger/R/utilities-print.R
geiger/R/diversitree.R
geiger/R/utilities-phylo.R
geiger/R/disparity.R
geiger/R/examples.R
geiger/R/medusa.R
geiger/R/likelihood.R
geiger/R/edges.R
geiger/R/traits-fossil.R
geiger/R/mecca.R
geiger/R/proposals.R
geiger/README.md
geiger/MD5
geiger/DESCRIPTION
geiger/ChangeLog
geiger/man
geiger/man/name.check.Rd
geiger/man/geiger-package.Rd
geiger/man/calibrate.mecca.Rd
geiger/man/fitContinuous.Rd
geiger/man/aicm.Rd
geiger/man/pp.mcmc.Rd
geiger/man/nodelabel.phylo.Rd
geiger/man/rc.Rd
geiger/man/startingpt.mecca.Rd
geiger/man/geiger-examples.Rd
geiger/man/geiger-defunct.Rd
geiger/man/sim.char.Rd
geiger/man/make.gbm.Rd
geiger/man/aicw.Rd
geiger/man/load.rjmcmc.Rd
geiger/man/fitContinuousMCMC.Rd
geiger/man/bd.ms.Rd
geiger/man/calibrate.rjmcmc.Rd
geiger/man/plot.medusa.Rd
geiger/man/nh.test.Rd
geiger/man/treedata.Rd
geiger/man/tips.Rd
geiger/man/sim.bd.Rd
geiger/man/dcount.Rd
geiger/man/sim.bdtree.Rd
geiger/man/to.auteur.Rd
geiger/man/drop.extinct.Rd
geiger/man/gbresolve.Rd
geiger/man/geiger-data.Rd
geiger/man/fitDiscrete.Rd
geiger/man/ratematrix.Rd
geiger/man/aov.phylo.Rd
geiger/man/congruify.phylo.Rd
geiger/man/rescale.Rd
geiger/man/mecca.Rd
geiger/man/subset.phylo.Rd
geiger/man/geiger-internal.Rd
geiger/man/rjmcmc.bm.Rd
geiger/man/dtt.Rd
geiger/man/medusa.Rd