API for liamrevell/phytools
Phylogenetic Tools for Comparative Biology (and Other Things)

Global functions
AIC.fitMk Source code
AIC.fitmultiMk Source code
AIC.ratebytree Source code
Diag Source code
Dtest Source code
EXPM Source code
MULTI2DI Source code
Map.Overlap Man page Source code
Qmatrix.from.gfit Source code
TREEDIST Source code
add.arrow Man page Source code
add.color.bar Man page Source code
add.everywhere Man page Source code
add.random Man page Source code
add.scalebar Source code
add.simmap.legend Man page Source code
add.species.to.genus Man page Source code
add.to.branches.and.nodes Source code
aic.w Man page Source code
allFurcTrees Man page Source code
allMatch Source code
allRotations Man page Source code
anc.BM Source code
anc.Bayes Man page Source code
anc.EB Source code
anc.ML Man page Source code
anc.OU Source code
anc.trend Man page Source code
ancThresh Man page Source code
anoletree Man page
apeAce Source code
applyBranchLengths Man page Source code
arc.cladelabels Man page Source code
as.multiPhylo Man page Source code
as.multiPhylo.multiSimmap Man page Source code
as.multiPhylo.phylo Man page Source code
as.phylo.simmap Source code
ave.rates Man page Source code
averageTree Man page Source code
backbone.toPhylo Man page Source code
backbone.toTrans Source code
bd Man page Source code
bind.tip Man page Source code
bind.tree.simmap Man page Source code
biplot.phyl.pca Man page Source code
bm Source code
bmPlot Man page Source code
bounce Source code
branch.and.bound Source code
branching.diffusion Man page Source code
brownie.lite Man page Source code
brownieREML Man page Source code
bySegments Source code
calcD Source code
check.pkg Source code
circles Source code
cladebox Source code
cladelabels Man page Source code
coef.phyl.RMA Man page Source code
collapse.to.star Man page Source code
collapseTree Man page Source code
compare.chronograms Man page Source code
compute.ancestor.nodes Source code
compute.mr Man page Source code
consensus.edges Man page Source code
contMap Man page Source code
cophylo Man page Source code
cospeciation Man page Source code
countSimmap Man page Source code
ctt Man page Source code
density.multiSimmap Man page Source code
densityMap Man page Source code
densityTree Man page Source code
describe.simmap Man page Source code
di2multi.simmap Man page Source code
dot.legend Man page Source code
dotTree Man page Source code
dotTree.continuous Source code
dotTree.discrete Source code
drawCurve Source code
drop.clade Man page Source code
drop.leaves Man page Source code
drop.tip.contMap Man page Source code
drop.tip.densityMap Man page Source code
drop.tip.simmap Man page Source code
drop.tip.singleton Man page Source code
droptipTree Source code
ebTree Source code
edgeProbs Man page Source code
edgelabels.cophylo Man page Source code
errorbar.contMap Man page Source code
estDiversity Man page Source code
evol.rate.mcmc Man page Source code
evol.vcv Man page Source code
evolvcv.lite Man page Source code
exhaustive.search Source code
exhaustiveMP Man page Source code
expand Source code
expand.clade Man page Source code
export.as.xml Man page Source code
extinctionTree Source code
extract.clade.simmap Man page Source code
extract.strahlerNumber Man page Source code
fan Source code
fancyTree Man page Source code
fastAnc Man page Source code
fastBM Man page Source code
fastDist Man page Source code
fastHeight Man page Source code
fastMRCA Man page Source code
findMRCA Man page Source code
fit.bd Man page Source code
fit.yule Man page Source code
fitBayes Man page Source code
fitDiversityModel Man page Source code
fitMk Man page Source code
fitPagel Man page Source code
fitmultiMk Man page Source code
fitted.multi.mantel Source code
foldtoLower Source code
force.ultrametric Man page Source code
fossilML Source code
gammatest Man page Source code
genSeq Man page Source code
genus.to.species.tree Man page Source code
geo.legend Man page Source code
get.asp Source code
get.treepos Man page Source code
getAncestors Source code
getBranch Source code
getChanges Source code
getCladesofSize Man page Source code
getDescendants Man page Source code
getEdgeLength Source code
getExtant Man page Source code
getExtinct Man page Source code
getLabel Source code
getParent Man page Source code
getPars Source code
getSisters Man page Source code
getState Source code
getStates Man page Source code
getnode Man page Source code
gtt Man page Source code
labelSubTree Source code
labelnodes Man page Source code
ladderize.simmap Man page Source code
lambda.transform Man page Source code
lambdaTree Source code Source code
lik.bd Man page Source code
lik.multiple Source code
lik.single Source code
likLiab Source code
likMlambda Man page Source code
likSurface.rateshift Man page Source code
likelihood.lambda Source code
linklabels Man page Source code
locate.fossil Man page Source code
locate.yeti Man page Source code
logLik.anc.trend Source code
logLik.fit.bd Source code
logLik.fitMk Source code
logLik.fitmultiMk Source code
logLik.multiSimmap Source code
logLik.pgls.Ives Source code
logLik.rateshift Source code
logLik.rerootingMethod Source code
logLik.simmap Source code
logMNORM Source code
logPrior Source code
ls.consensus Man page Source code
ls.tree Man page Source code
ltt Man page Source code
ltt95 Man page Source code
make.era.map Man page Source code
make.simmap Man page Source code
make.sym Source code
make.transparent Man page Source code
makeMappedEdge Source code
makelinks Source code
map.overlap Man page Source code
map.to.singleton Man page Source code
mapped.states Man page Source code
markChanges Man page Source code
matchDatatoTree Source code
matchLabels Man page Source code
matchNodes Man page Source code
matchTreetoData Source code
matchType Source code
maxLambda Source code
mcmcBM Source code
mcmcBM.full Source code
mcmcLambda Source code
mcmcMk Man page Source code
mcmcQ Source code
mergeAdjacent Source code
mergeMappedStates Man page Source code
midpoint.root Man page Source code
minRotate Man page Source code
minSplit Man page Source code
minTreeDist Man page Source code
modified.Grafen Man page Source code
mrp.supertree Man page Source code
multi.mantel Man page Source code
multiC Man page Source code
multiOU Man page Source code
multiRF Man page Source code
namesplit Source code
newick Source code
node.paths Man page Source code
nodeHeights Man page Source code
nodeheight Man page Source code
nodelabels.cophylo Man page Source code
optim.phylo.ls Man page Source code
orderMappedEdge Man page Source code
paintBranches Man page Source code
paintSubTree Man page Source code
paste.tree Man page Source code
pbtree Man page Source code
pgls.Ives Man page Source code
pgls.SEy Man page Source code
phenogram Man page Source code
phenogram95 Source code
phyl.RMA Man page Source code
phyl.cca Man page Source code
phyl.pairedttest Man page Source code
phyl.pca Man page Source code
phyl.resid Man page Source code
phyl.vcv Man page Source code
phylANOVA Man page Source code
phylo.heatmap Man page Source code
phylo.to.map Man page Source code
phylo.toBackbone Man page Source code
phyloDesign Man page Source code
phyloScattergram Source code
phylogram Source code
phylomorphospace Man page Source code
phylomorphospace3d Man page Source code
phylosig Man page Source code
phytools Man page
phytools-package Man page
plot.anc.Bayes Source code
plot.ancThresh Source code
plot.backbonePhylo Man page Source code
plot.changesMap Man page Source code
plot.contMap Man page Source code
plot.cophylo Man page Source code
plot.cospeciation Man page Source code
plot.ctt Source code
plot.densityMap Man page Source code
plot.describe.simmap Man page Source code
plot.expand.clade Man page Source code
plot.fitBayes Source code
plot.fitMk Man page Source code
plot.fitPagel Man page Source code
plot.gfit Man page Source code
plot.gtt Source code
plot.ltt Source code
plot.ltt95 Man page Source code
plot.multiCophylo Source code
plot.multiCtt Source code
plot.multiLtt Source code
plot.multiSimmap Man page Source code
plot.phyl.RMA Man page Source code
plot.phyl.pca Source code
plot.phylo.to.map Man page Source code
plot.phyloScattergram Source code
plot.rateshift Man page Source code
plot.rerootingMethod Source code
plot.simmap Man page Source code
plot.threshBayes Source code
plotBranchbyTrait Man page Source code
plotCladogram Source code
plotContMap Source code
plotDensityMap Source code
plotFan Source code
plotPhylogram Source code
plotSimmap Man page Source code
plotThresh Man page Source code
plotTree Man page Source code
plotTree.barplot Man page Source code
plotTree.boxplot Man page Source code
plotTree.datamatrix Man page Source code
plotTree.errorbars Man page Source code
plotTree.singletons Man page Source code
plotTree.splits Man page Source code
plotTree.wBars Man page Source code
posterior.evolrate Man page Source code
posthoc Man page Source code
posthoc.ratebytree Man page Source code
prbt.cont Source code
prbt.disc Source code
prbt.div Source code
print.aic.w Source code
print.anc.Bayes Source code
print.anc.ML Source code
print.anc.trend Source code
print.ancThresh Source code
print.backbonePhylo Man page Source code
print.brownie.lite Source code
print.brownieREML Source code
print.changesMap Source code
print.contMap Source code
print.cophylo Source code
print.cospeciation Man page Source code
print.ctt Source code
print.densityMap Source code
print.describe.simmap Source code
print.evol.rate.mcmc Source code
print.evol.vcv Source code
print.evolvcv.lite Source code
print.expand.clade Source code
print.fastAnc Source code
print.fit.bd Man page Source code
print.fitBayes Source code
print.fitMk Source code
print.fitPagel Source code
print.fitmultiMk Source code
print.gtt Source code
print.ltt Source code
print.ltt95 Source code
print.mcmcMk Source code
print.multi.mantel Source code
print.multiCophylo Source code
print.multiCtt Source code
print.multiLtt Source code
print.multiSimmap Source code
print.pgls.Ives Source code
print.phyl.RMA Source code
print.phyl.cca Source code
print.phyl.pairedttest Source code
print.phyl.pca Source code
print.phylANOVA Source code
print.phylo.to.map Source code
print.phyloScattergram Source code
print.posthoc.ratebytree Source code
print.ratebystate Source code
print.ratebytree Source code
print.rateshift Source code
print.rerootingMethod Source code
print.simmap Source code
print.threshBayes Source code
printDotDot Source code
printmessage Source code
probMatch Source code
project.phylomorphospace Man page Source code
qb Source code
qpd Source code
ratebystate Man page Source code
ratebytree Man page Source code
rateshift Man page Source code
rbt.cont Source code
rbt.disc Source code
rbt.div Source code
read.newick Man page Source code
read.simmap Man page Source code
readNexusData Source code
remlMlambda Source code
reorder.backbonePhylo Man page Source code
reorder.simmap Source code
reorderPhylo Source code
reorderSimmap Man page Source code
rep.multiPhylo Man page Source code
rep.phylo Man page Source code
repPhylo Man page Source code
reroot Man page Source code
rerootingMethod Man page Source code
rescaleSimmap Man page Source code
rescaleTree Source code
residuals.multi.mantel Source code
residuals.phyl.RMA Source code
resolveAllNodes Man page Source code
resolveNode Man page Source code
rootedge.to.singleton Man page Source code
rotate.multi Man page Source code
rotateNodes Man page Source code
round.polygon Source code
roundBranches Man page Source code
roundPhylogram Man page Source code
rss Source code
rstate Man page Source code
sampleFrom Man page Source code
scaleByMap Source code
scaleN Source code
sch Source code
setMap Man page Source code
sim.Mk Man page Source code
sim.corrs Man page Source code
sim.ctt Man page Source code
sim.history Man page Source code
sim.multiCtt Man page Source code
sim.multiMk Man page Source code
sim.ratebystate Man page Source code
sim.rates Man page Source code
simBM Source code
simOU Source code
skewers Man page Source code
smap Source code
splitEdgeColor Man page Source code
splitTree Man page Source code
splitplotTree Man page Source code
spreadlabels Source code
starTree Man page Source code
statdist Source code
strahlerNumber Man page Source code
summary.cophylo Source code
summary.fitMk Source code
summary.fitmultiMk Source code
summary.multiSimmap Man page Source code
summary.phyl.pca Source code
summary.simmap Man page Source code
tTests Source code
text_to_tree Source code
th Source code
threshBayes Man page Source code
threshCol Source code
threshDIC Man page Source code
threshState Man page
tipRotate Man page Source code
tiplabels.cophylo Man page Source code
to.matrix Man page Source code Source code
to.symmetric Source code
to.upper Source code
to.vector Source code
traitgram3d Source code
treeSlice Man page Source code
unfoldLower Source code
untangle Man page Source code
updownPhylogram Source code
upper.diag Source code
vcvPhylo Man page Source code
whichorder Source code
write.simmap Man page Source code
writeAnc Source code
writeAncestors Man page Source code
writeNex Source code
writeNexus Man page Source code
yetiML Source code
yetiREML Source code
liamrevell/phytools documentation built on May 28, 2018, 7:14 p.m.