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

Functions

aicm Man page
aicw Man page
amphibia Man page
aov.phylo Man page
area.between.curves Man page
argn Man page
argn<- Man page
argn<-.bm Man page
argn.bm Man page
argn.default Man page
argn.mkn Man page
as.phylo.hphylo Man page
bd.km Man page
bd.ms Man page
BDsim Man page
bf Man page
birthdeath.tree Man page
bm.lik Man page
calibrate.mecca Man page
calibrate.proposalwidth Man page
calibrate.rjmcmc Man page
caniformia Man page
carnivores Man page
caudata Man page
chelonia Man page
cherries Man page
coef.gfit Man page
coef.gfits Man page
compare.rates Man page
congruify.phylo Man page
constrain Man page
constrain.k Man page
constrain.m Man page
crown.limits Man page
crown.p Man page
dcount Man page
deltaTree Man page
disparity Man page
disp.calc Man page
dlunif Man page
drop.extinct Man page
drop.random Man page
drop.tip Man page
dtpois Man page
dtt Man page
dtt.full Man page
edgelabels.auteur Man page
edges.phylo Man page
ess Man page
exemplar.phylo Man page
ex.jumpsimulator Man page
exponentialchangeTree Man page
ex.ratesimulator Man page
ex.traitgram Man page
fitContinuous Man page
fitContinuousMCMC Man page
fitDiscrete Man page
fitDiversification Man page
fitSplitModel Man page
gbcontain Man page
gbresolve Man page
gbresolve.default Man page
gbresolve.phylo Man page
gbtaxdump Man page
geiger Man page
geiger-package Man page
gen Man page
geospiza Man page
getAncStates Man page
getBD Man page
getDiversificationModel Man page
getFullSplitModel Man page
get.simulation.matrix Man page
glomogram.phylo Man page
hashes.phylo Man page
hashes.rjmcmc Man page
hash.node Man page
hdr Man page
heights Man page
heights.multiPhylo Man page
heights.phylo Man page
hme Man page
ic.sigma Man page
intercalate.samples Man page
is.constrained Man page
is.extinct Man page
is.phylo Man page
is.root Man page
kappaTree Man page
kendallmoran.rate Man page
lambdaTree Man page
likfx.bm Man page
linearchangeTree Man page
Linnaean Man page
load Man page
load.rjmcmc Man page
logLik.gfit Man page
logLik.gfits Man page
lookup.phylo Man page
make.bm.relaxed Man page
make.gbm Man page
mecca Man page
medusa Man page
mkn.lik Man page
name.check Man page
nh.test Man page
nodelabel.phylo Man page
node.leaves Man page
node.sons Man page
ouTree Man page
PATHd8.phylo Man page
phy.anova Man page
phylo.clades Man page
phylo.lookup Man page
phy.manova Man page
plot.auteurMCMC Man page
plot.auteurMCMCMC Man page
plotDiversificationSurface Man page
plot.medusa Man page
plot.rjmcmc Man page
plot.rjmcmc.list Man page
pool.rjmcmcsamples Man page
pp.mcmc Man page
primates Man page
print.auteurRAW Man page
print.bayesfactor Man page
print.bm Man page
print.constraint.m Man page
print.glnL Man page
print.gprior Man page
print.mcmc.list Man page
print.medusa Man page
print.mkn Man page
print.rbm Man page
print.rjmcmc Man page
print.rjmcmcmc Man page
print.taxdump Man page
print.transformer Man page
prune.extinct.taxa Man page
prune.random.taxa Man page
rate.estimate Man page
ratematrix Man page
rc Man page
rescale Man page
rescale.phylo Man page
rescaleTree Man page
resplitEdgeMatrixGeiger Man page
rjmcmc.bm Man page
root.phylo Man page
runMedusa Man page
sem Man page
shifts.plot Man page
sim.bd Man page
sim.bdtree Man page
sim.char Man page
sim.mecca Man page
span.phylo Man page
speciationalTree Man page
splitEdgeMatrixGeiger Man page
startingpt.mecca Man page
stem.limits Man page
stem.p Man page
subset.phylo Man page
tip.disparity Man page
tips Man page
to.auteur Man page
to.coda Man page
tracer Man page
transform.phylo Man page
treedata Man page
tworateTree Man page
ultrametricize.phylo Man page
unique.multiPhylo Man page
unique.phylo Man page
vmat Man page
whales Man page
white.mkn Man page
write.pathd8 Man page
write.r8s Man page
write.treePL Man page

Files

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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