ouch: Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses
Version 2.9-1

Fit and compare Ornstein-Uhlenbeck models for evolution along a phylogenetic tree.

Browse man pages Browse package API and functions Browse package files

AuthorAaron A. King <kingaa@umich.edu> and Marguerite A. Butler <mbutler@hawaii.edu>
Date of publication2015-06-04 19:27:11
MaintainerAaron A. King <kingaa@umich.edu>
LicenseGPL(>= 2)
Version2.9-1
URL http://ouch.r-forge.r-project.org/
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ouch", repos="http://R-Forge.R-project.org")

Man pages

anolis.ssd: Greater Antillean anolis lizard sexual size dimorphism data.
ape2ouch: Convert an "ape" tree to an "ouch" tree.
bimac: Anolis bimaculatus lizard size data.
brown: Fit a Brownian-motion model of evolution along a phylogenetic...
browntree-class: Fitted phylogenetic Brownian motion model
hansen: Hansen model of evolution along a phylogenetic tree
hansentree-class: hansen tree object
hansentree-methods: Methods of the "hansentree" class
ouch-package: Ornstein-Uhlenbeck methods for comparative phylogenetic...
ouchtree-class: Phylogenetic tree object in 'ouch' format.
paint: Painting selective regimes on a phylogenetic tree.

Functions

ancestor.numbers Source code
anolis.ssd Man page
ape2ouch Man page Source code
arrange.tree Source code
as,hansentree-method Man page
bimac Man page
bootstrap Man page Source code
bootstrap,browntree-method Man page
bootstrap,hansentree-method Man page
bootstrap-browntree Man page
bootstrap-hansentree Man page
branch.height Source code
branch.times Source code
brown Man page Source code
brown.deviate Source code
browntree Man page
browntree-class Man page
build.lineages Source code
coef,browntree-method Man page
coef,hansentree-method Man page
coef-browntree Man page
coef-hansentree Man page
coerce,browntree,data.frame-method Man page
coerce,hansentree,data.frame-method Man page
coerce,ouchtree,data.frame-method Man page
epochs Source code
glssoln Source code
hansen Man page Source code
hansen.deviate Source code
hansentree Man page
hansentree-class Man page
hansentree-methods Man page
is.root.node Source code
logLik,browntree-method Man page
logLik,hansentree-method Man page
logLik-browntree Man page
logLik-hansentree Man page
ou.lik.fn Source code
ouch-package Man page
ouchtree Man page Source code
ouchtree-class Man page
paint Man page Source code
plot,browntree-method Man page
plot,hansentree-method Man page
plot,ouchtree-method Man page
plot-browntree Man page
plot-hansentree Man page
plot-ouchtree Man page
print,browntree-method Man page
print,hansentree-method Man page
print,ouchtree-method Man page
print-browntree Man page
print-hansentree Man page
print-ouchtree Man page
regime.spec Source code
rmvnorm Source code
sets.of.regimes Source code
show,browntree-method Man page
show,hansentree-method Man page
show,ouchtree-method Man page
show-browntree Man page
show-hansentree Man page
show-ouchtree Man page
simulate,browntree-method Man page
simulate,hansentree-method Man page
simulate-browntree Man page
simulate-hansentree Man page
summary,browntree-method Man page
summary,hansentree-method Man page
summary-browntree Man page
summary-hansentree Man page
sym.par Source code
sym.solve Source code
sym.unpar Source code
terminal.twigs Source code
tree.plot.internal Source code
update,browntree-method Man page
update,hansentree-method Man page
update-browntree Man page
update-hansentree Man page

Files

DESCRIPTION
NAMESPACE
R
R/ape2ouch.R
R/brown.R
R/glssoln.R
R/hansen.R
R/methods.R
R/ouchtree.R
R/paint.R
R/plot.R
R/rmvnorm.R
data
data/anolis.ssd.csv.gz
data/bimac.csv.gz
inst
inst/CITATION
inst/ChangeLog
inst/GPL
inst/NEWS
inst/NEWS.Rd
inst/OCHANGELOG
man
man/anolis.ssd.Rd
man/ape2ouch.Rd
man/bimac.Rd
man/brown.Rd
man/browntree-class.Rd
man/hansen.Rd
man/hansentree-class.Rd
man/hansentree-methods.Rd
man/ouch-package.Rd
man/ouchtree-class.Rd
man/paint.Rd
src
src/covar-matrix.c
src/ouch.h
src/weight-matrix.c
tests
tests/boot.R
tests/boot.Rout.save
tests/exacttree.R
tests/exacttree.Rout.save
tests/simtree.R
tests/simtree.Rout.save
ouch documentation built on May 21, 2017, 4:15 a.m.