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Latest commit c267edc Dec 29, 2016 @liamrevell S3 methods for phyl.RMA
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add.arrow.Rd Initial commit Aug 18, 2015
add.color.bar.Rd updates to plot method for densityMap and contMap Feb 17, 2016
add.everywhere.Rd Initial commit Aug 18, 2015
add.random.Rd Initial commit Aug 18, 2015
add.simmap.legend.Rd Initial commit Aug 18, 2015
add.species.to.genus.Rd new function to simulate species-level subtrees under a Yule process … Nov 4, 2015
aic.w.Rd update version number & some man pages Dec 6, 2016
allFurcTrees.Rd Initial commit Aug 18, 2015
anc.Bayes.Rd Initial commit Aug 18, 2015
anc.ML.Rd Initial commit Aug 18, 2015
anc.trend.Rd Initial commit Aug 18, 2015
ancThresh.Rd Initial commit Aug 18, 2015
anoletree.Rd Initial commit Aug 18, 2015
applyBranchLengths.Rd Initial commit Aug 18, 2015
as.multiPhylo.Rd as.multiPhylo for phylo object Dec 28, 2016
ave.rates.Rd Initial commit Aug 18, 2015
averageTree.Rd update to roundPhylogram and ls.consensus Jun 11, 2016
bd.Rd fix man page for bd Dec 3, 2016
bind.tip.Rd interactive mode for bind.tip Oct 31, 2015
bind.tree.simmap.Rd bind.tree for simmap objects May 20, 2016
bmPlot.Rd Initial commit Aug 18, 2015
branching.diffusion.Rd Initial commit Aug 18, 2015
brownie.lite.Rd Initial commit Aug 18, 2015
brownieREML.Rd modification to deal with optimization issues Sep 24, 2015
cladelabels.Rd Initial commit Aug 18, 2015
collapse.to.star.Rd update to collapse.to.star to permit no edge lengths Oct 7, 2015
collapseTree.Rd update to collapseTree documentation Sep 7, 2015
consensus.edges.Rd new functions for consensus trees or average trees Apr 7, 2016
contMap.Rd updates to plot method for densityMap and contMap Feb 17, 2016
cophylo.Rd update version number & some man pages Dec 6, 2016
cospeciation.Rd fixes for Rcmd check Nov 29, 2016
countSimmap.Rd Initial commit Aug 18, 2015
densityMap.Rd updates to plot method for densityMap and contMap Feb 17, 2016
densityTree.Rd fixes to documentation files & NAMESPACE May 30, 2016
describe.simmap.Rd add aliases & function definition for summary & plot methods for simm… Mar 20, 2016
di2multi.simmap.Rd update to S3 method documentation in di2multi.simmap Dec 3, 2016
dotTree.Rd updates to dotTree May 26, 2016
drop.clade.Rd Initial commit Aug 18, 2015
drop.leaves.Rd Initial commit Aug 18, 2015
drop.tip.contMap.Rd Initial commit Aug 18, 2015
drop.tip.simmap.Rd Initial commit Aug 18, 2015
edgeProbs.Rd new function to compute the probabilities of changes along edges of t… Nov 11, 2015
estDiversity.Rd Initial commit Aug 18, 2015
evol.rate.mcmc.Rd Initial commit Aug 18, 2015
evol.vcv.Rd Initial commit Aug 18, 2015
evolvcv.lite.Rd Initial commit Aug 18, 2015
exhaustiveMP.Rd Initial commit Aug 18, 2015
expm.Rd Initial commit Aug 18, 2015
export.as.xml.Rd Initial commit Aug 18, 2015
fancyTree.Rd Initial commit Aug 18, 2015
fastAnc.Rd option to fix some internal nodes in fastAnc Nov 6, 2015
fastBM.Rd Initial commit Aug 18, 2015
fastMRCA.Rd various updates to allow control of color bar width in contMap & dens… Dec 9, 2015
findMRCA.Rd update findMRCA to use ape::getMRCA internally Dec 25, 2016
fitBayes.Rd Initial commit Aug 18, 2015
fitDiversityModel.Rd Initial commit Aug 18, 2015
fitMk.Rd plot method for fitDiscrete Jun 1, 2016
fitPagel.Rd update doc & NAMESPACE May 31, 2016
gammatest.Rd Initial commit Aug 18, 2015
genSeq.Rd Initial commit Aug 18, 2015
getCladesofSize.Rd Initial commit Aug 18, 2015
getDescendants.Rd Initial commit Aug 18, 2015
getExtant.Rd Initial commit Aug 18, 2015
getSisters.Rd Initial commit Aug 18, 2015
getStates.Rd Initial commit Aug 18, 2015
ladderize.simmap.Rd Initial commit Aug 18, 2015
lambda.transform.Rd Initial commit Aug 18, 2015
likMlambda.Rd Initial commit Aug 18, 2015
locate.fossil.Rd Initial commit Aug 18, 2015
locate.yeti.Rd Initial commit Aug 18, 2015
ls.tree.Rd Initial commit Aug 18, 2015
ltt.Rd Initial commit Aug 18, 2015
ltt95.Rd Initial commit Aug 18, 2015
make.era.map.Rd Initial commit Aug 18, 2015
make.simmap.Rd Initial commit Aug 18, 2015
map.overlap.Rd fix typo in map.overlap.Rd Apr 17, 2016
map.to.singleton.Rd changes to nodeHeights & other functions with regard to root.edge Feb 8, 2016
mapped.states.Rd new function mapped.states Mar 21, 2016
markChanges.Rd Initial commit Aug 18, 2015
matchNodes.Rd new function matchLabels Mar 8, 2016
mergeMappedStates.Rd Initial commit Aug 18, 2015
midpoint.root.Rd Initial commit Aug 18, 2015
minRotate.Rd update to cophylo & minRotate documentation Aug 13, 2016
minSplit.Rd Initial commit Aug 18, 2015
modified.Grafen.Rd new function to compute modified Grafen edge lengths Nov 2, 2016
mrp.supertree.Rd update to mrp.supertree.R to allow the matrix representation of the t… Nov 26, 2015
multi.mantel.Rd Initial commit Aug 18, 2015
multiC.Rd multiC with internal nodes Jun 6, 2016
multiRF.Rd Initial commit Aug 18, 2015
nodeHeights.Rd changes to nodeHeights & other functions with regard to root.edge Feb 8, 2016
nodelabels.cophylo.Rd add nodelabels.cophylo to NAMESPACE & add man page Oct 23, 2015
optim.phylo.ls.Rd Initial commit Aug 18, 2015
orderMappedEdge.Rd Initial commit Aug 18, 2015
paintSubTree.Rd Initial commit Aug 18, 2015
paste.tree.Rd Initial commit Aug 18, 2015
pbtree.Rd small update to pbtree doc Dec 9, 2015
pgls.Ives.Rd Initial commit Aug 18, 2015
phenogram.Rd add dontrun to phenogram doc Jun 24, 2016
phyl.RMA.Rd S3 methods for phyl.RMA Dec 29, 2016
phyl.cca.Rd Initial commit Aug 18, 2015
phyl.pairedttest.Rd Initial commit Aug 18, 2015
phyl.pca.Rd Initial commit Aug 18, 2015
phyl.resid.Rd Initial commit Aug 18, 2015
phyl.vcv.Rd Initial commit Aug 18, 2015
phylANOVA.Rd Initial commit Aug 18, 2015
phylo.heatmap.Rd fix doc typos Feb 17, 2016
phylo.to.map.Rd fix to doc phylo.to.map Jun 5, 2016
phylo.toBackbone.Rd Initial commit Aug 18, 2015
phyloDesign.Rd Initial commit Aug 18, 2015
phylomorphospace.Rd Initial commit Aug 18, 2015
phylomorphospace3d.Rd Initial commit Aug 18, 2015
phylosig.Rd Initial commit Aug 18, 2015
phytools-package.Rd Initial commit Aug 18, 2015
plot.backbonePhylo.Rd update to backbonePhylo methods and doc Jul 14, 2016
plotBranchbyTrait.Rd small update to plotBranchbyTrait to allow palette to be specified as… Dec 7, 2016
plotSimmap.Rd add user control of lend to plotSimmap & plot.simmap Nov 11, 2016
plotThresh.Rd Initial commit Aug 18, 2015
plotTree.Rd Initial commit Aug 18, 2015
plotTree.wBars.Rd small fixes to cophylo and doc Aug 12, 2016
posterior.evolrate.Rd Initial commit Aug 18, 2015
print.backbonePhylo.Rd Initial commit Aug 18, 2015
ratebystate.Rd Initial commit Aug 18, 2015
rateshift.Rd update version number & some man pages Dec 6, 2016
read.newick.Rd add functionality in read.newick to pass arguments to scan Dec 20, 2015
read.simmap.Rd Initial commit Aug 18, 2015
reorder.backbonePhylo.Rd Initial commit Aug 18, 2015
reorderSimmap.Rd Initial commit Aug 18, 2015
rep.phylo.Rd Initial commit Aug 18, 2015
reroot.Rd change default when argument position not supplied Feb 18, 2016
rerootingMethod.Rd modification to fitPagel to use fitMk internally Sep 18, 2015
rescaleSimmap.Rd Initial commit Aug 18, 2015
resolveNode.Rd fix man for resolveNode Aug 9, 2016
rotateNodes.Rd new function to compute all node rotations Aug 28, 2016
roundBranches.Rd Initial commit Aug 18, 2015
roundPhylogram.Rd update to roundPhylogram and ls.consensus Jun 11, 2016
rstate.Rd Initial commit Aug 18, 2015
sampleFrom.Rd Initial commit Aug 18, 2015
setMap.Rd Initial commit Aug 18, 2015
sim.corrs.Rd Initial commit Aug 18, 2015
sim.history.Rd fix/update to sim.history for setting anc May 11, 2016
sim.ratebystate.Rd Initial commit Aug 18, 2015
sim.rates.Rd Initial commit Aug 18, 2015
skewers.Rd Initial commit Aug 18, 2015
splitEdgeColor.Rd man page for splitEdgeColor Sep 5, 2015
splitTree.Rd Initial commit Aug 18, 2015
splitplotTree.Rd Initial commit Aug 18, 2015
starTree.Rd Initial commit Aug 18, 2015
strahlerNumber.Rd Initial commit Aug 18, 2015
threshBayes.Rd Initial commit Aug 18, 2015
threshDIC.Rd Initial commit Aug 18, 2015
threshState.Rd Initial commit Aug 18, 2015
to.matrix.Rd Initial commit Aug 18, 2015
treeSlice.Rd typo correction to treeSlice.Rd Aug 18, 2015
untangle.Rd Initial commit Aug 18, 2015
vcvPhylo.Rd Initial commit Aug 18, 2015
write.simmap.Rd remove example from write.simmap, update NAMESPACE Dec 9, 2015
writeAncestors.Rd Initial commit Aug 18, 2015
writeNexus.Rd Initial commit Aug 18, 2015