geiger: Analysis of evolutionary diversification
- CRAN: http://cran.r-project.org/web/packages/geiger/index.html
- URL: http://www.webpages.uidaho.edu/~lukeh/software.html
- URL: http://informatics.nescent.org/wiki
> library(geiger)
バージョン: 2.0.3
| 関数名 | 概略 |
|---|---|
aicm |
Akaike's Information Criterion for MCMC samples (AICM) |
aicw |
determining Akaike weights |
amphibia |
example datasets |
aov.phylo |
phylogenetic ANOVA and MANOVA |
area.between.curves |
deprecated functions in GEIGER |
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 |
ex.traitgram |
internal geiger functions |
fitContinuous |
model fitting for continuous comparative data |
fitContinuousMCMC |
Fit models of continuous trait evolution to comparative data using MCMC |
fitDiscrete |
model fitting for discrete comparative data |
gbresolve |
NCBI taxonomy |
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 AIC |
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 AIC |
pp.mcmc |
using posterior predictive MCMC for modeling quantitative trait evolution |
print.bm |
internal geiger functions |
ratematrix |
evolutionary VCV matrix |
rc |
relative cladogenesis test |
rescale |
Tree transformations |
rjmcmc.bm |
Bayesian sampling of shifts in trait evolution: relaxed Brownian motion |
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 |