geiger v2.0.6.2

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Analysis of Evolutionary Diversification

Methods for fitting macroevolutionary models to phylogenetic trees.

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Geiger

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This is the development version of the geiger package for manipulating phylogenetic comparative data and fitting macroevolutionary models. The package can be downloaded from CRAN

install.packages("geiger")

or installed directly from github with the devtools package

install.packages("devtools")
install_github("mwpennell/geiger-v2")

Major features

geiger is a (growing) collection of methods developed over the years by many researchers. Here is a a non-comprehensive list of methods:

Citing geiger

If you use geiger, please cite:

Pennell, M.W., J.M. Eastman, G.J. Slater, J.W. Brown, J.C. Uyeda, R.G. FitzJohn, M.E. Alfaro, and L.J. Harmon. 2014. geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. Bioinformatics 15:2216-2218.

in addition to the original papers describing the methods.

Feedback

We are always looking to improve geiger. If you have comments/questions/ideas, we encourage you to get in contact by posting an issue or making a pull request.

Functions in geiger

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

Type Package
Date 2015-09-07
LinkingTo Rcpp
License GPL (>= 2)
URL http://www.webpages.uidaho.edu/~lukeh/software.html
ByteCompile yes
NeedsCompilation yes
Packaged 2019-06-04 09:54:12 UTC; ripley
Repository CRAN
Date/Publication 2019-06-04 10:19:01 UTC
X-CRAN-Original-Maintainer Matt Pennell
X-CRAN-Comment Orphaned and corrected on 2019-01-16 as no response to request for corrections.

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