geiger: Analysis of Evolutionary Diversification

Methods for fitting macroevolutionary models to phylogenetic trees.

AuthorLuke 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 publication2015-09-07 21:26:42
MaintainerMatt Pennell <mwpennell@gmail.com>
LicenseGPL (>= 2)
Version2.0.6
http://www.webpages.uidaho.edu/~lukeh/software.html

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

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