iteRates: Parametric rate comparison
Version 3.1

Iterates through a phylogenetic tree to identify regions of rate variation using the parametric rate comparison test.

Browse man pages Browse package API and functions Browse package files

AuthorPremal Shah, Benjamin Fitzpatrick, James Fordyce
Date of publication2013-05-03 21:40:36
MaintainerBen Fitzpatrick <benfitz@utk.edu>
LicenseGPL (>= 3)
Version3.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("iteRates")

Man pages

color.tree.plot: color.tree.plot
comp.fit.subs: comp.fit.subs
comp.subs: comp.subs
fp.comp.subs: FP.comp.subs
id.subtrees: id.subtrees
iterates-package: iteRates
tab.summary: tab.summary
tree.na.count: tree.na.Count
tree.rand.test: tree.rand.test
trimtree: trimTree

Functions

BOTHlabels2 Source code
CompareSubTrees.k Source code
FP.comp.subs Man page Source code
GroupsAsText Source code
Null.comp.subs.ef Source code
PosGroups Source code
Qcomp.subs Source code
RemRedun Source code
SetUpGroupMatrix Source code
SumSetUpGroupMatrix Source code
birthdeath.tree.geiger1.3.1 Source code
calc.rate.lnorm Source code
calc.rate.vrat Source code
calc.rate.weib Source code
calcClus Source code
censor.exp.x Source code
censor.lnorm.x Source code
censor.vrat.x Source code
censor.weib.x Source code
class.edge.all Source code
color.tree.plot Man page Source code
comBim Source code
comp.fit.subs Man page Source code
comp.subs Man page Source code
comp.subs.DF Source code
compareSubTrees Source code
drop.tip2.6 Source code
edgelabels2 Source code
id.subtrees Man page Source code
internds Source code
iteRates Man page
iteRates-package Man page
mergelist Source code
min.lnorm Source code
min.vrat Source code
min.weib Source code
model.sel.distbn Source code
node.sons Source code
phylogram.plot2 Source code
plot.phylo2 Source code
posClusters Source code
remainingTax Source code
subtrees2.6 Source code
subtreez Source code
tab.summary Man page Source code
tab.table Source code
tree.na.Count Man page Source code
tree.rand.test Man page Source code
treeSims Source code
trimTree Man page Source code
tt.Summary Source code

Files

R
R/tt.Summary.R
R/trimTree.R
R/treeSims.R
R/tree.rand.test.R
R/tree.na.Count.R
R/tab.table.R
R/tab.summary.R
R/SumSetUpGroupMatrix.R
R/subtreez.R
R/subtrees2.6.R
R/SetUpGroupMatrix.R
R/RemRedun.R
R/remainingTax.R
R/Qcomp.subs.R
R/PosGroups.R
R/posClusters.R
R/plot.phylo2.R
R/phylogram.plot2.R
R/Null.comp.subs.ef.R
R/node.sons.R
R/model.sel.distbn.R
R/min.weib.R
R/min.vrat.R
R/min.lnorm.R
R/mergelist.R
R/internds.R
R/id.subtrees.R
R/GroupsAsText.R
R/FP.comp.subs.R
R/edgelabels2.R
R/drop.tip2.6.R
R/compareSubTrees.R
R/CompareSubTrees.k.R
R/comp.subs.R
R/comp.subs.DF.R
R/comp.fit.subs.R
R/comBim.R
R/color.tree.plot.R
R/class.edge.all.R
R/censor.weib.x.R
R/censor.vrat.x.R
R/censor.lnorm.x.R
R/censor.exp.x.R
R/calcClus.R
R/calc.rate.weib.R
R/calc.rate.vrat.R
R/calc.rate.lnorm.R
R/BOTHlabels2.R
R/birthdeath.tree.geiger1.3.1.R
NAMESPACE
MD5
man
man/trimtree.rd
man/tree.rand.test.Rd
man/tree.na.count.rd
man/tab.summary.rd
man/iterates-package.rd
man/id.subtrees.rd
man/fp.comp.subs.rd
man/comp.subs.Rd
man/comp.fit.subs.Rd
man/color.tree.plot.Rd
DESCRIPTION
iteRates documentation built on May 19, 2017, 10:04 p.m.