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add.everywhere.R Initial commit Aug 18, 2015
add.random.R Initial commit Aug 18, 2015
add.species.to.genus.R user supplied internal node states in contMap Nov 5, 2015
allFurcTrees.R Initial commit Aug 18, 2015
anc.Bayes.R Initial commit Aug 18, 2015
anc.ML.R small add'l fix to anc.ML Aug 15, 2016
anc.trend.R Initial commit Aug 18, 2015
ancThresh.R Initial commit Aug 18, 2015
backbonePhylo.R update to backbonePhylo methods and doc Jul 14, 2016
bmPlot.R Initial commit Aug 18, 2015
branching.diffusion.R Initial commit Aug 18, 2015
brownie.lite.R Initial commit Aug 18, 2015
brownieREML.R correct messaging in brownieREML Sep 24, 2015
collapseTree.R new function aic.w Dec 3, 2016
consensus.edges.R fix to consensus.edge, update to evol.vcv Jun 19, 2016
contMap.R handy fix to contMap & densityMap for short internal edges Jun 7, 2016
cophylo.R fix to attribute of tipRotate value returned by exhaustive method Jan 10, 2017
cospeciation.R new method for cospeciation testing Nov 1, 2016
densityMap.R fix date on source nodes Jun 8, 2016
densityTree.R new function Map.Overlap Apr 17, 2016
dotTree.R fix to permit dotTree to work with new plotrix Jun 5, 2016
drop.tip.simmap.R Initial commit Aug 18, 2015
estDiversity.R Initial commit Aug 18, 2015
evol.rate.mcmc.R Initial commit Aug 18, 2015
evol.vcv.R fix to consensus.edge, update to evol.vcv Jun 19, 2016
evolvcv.lite.R Initial commit Aug 18, 2015
exhaustiveMP.R Initial commit Aug 18, 2015
export.as.xml.R Initial commit Aug 18, 2015
fancyTree.R fixes for Rcmd check Nov 29, 2016
fastAnc.R small bug work-around in fastAnc Nov 28, 2015
fastBM.R Initial commit Aug 18, 2015
fitBayes.R Initial commit Aug 18, 2015
fitDiversityModel.R Initial commit Aug 18, 2015
fitMk.R update to fitMk for more user control of optimization Sep 20, 2016
fitPagel.R lots of further updates to S3 plotting method for fitPagel May 30, 2016
locate.fossil.R Initial commit Aug 18, 2015
locate.yeti.R Initial commit Aug 18, 2015
ls.consensus.R add comma to message Jun 13, 2016
ltt.R Initial commit Aug 18, 2015
ltt95.R Initial commit Aug 18, 2015
make.era.map.R Initial commit Aug 18, 2015
make.simmap.R fixes for Rcmd check Nov 29, 2016
map.overlap.R new function Map.Overlap Apr 17, 2016
map.to.singleton.R changes to nodeHeights & other functions with regard to root.edge Feb 8, 2016
mcmcBM.R Initial commit Aug 18, 2015
mcmcBM.full.R Initial commit Aug 18, 2015
mcmcLambda.R Initial commit Aug 18, 2015
mrp.supertree.R small change to permit compute.mr with single tree Nov 26, 2015
multi.mantel.R Initial commit Aug 18, 2015
multiRF.R Initial commit Aug 18, 2015
optim.phylo.ls.R totally re-wrote phyloDesign to be much faster Oct 12, 2015
paintSubTree.R Initial commit Aug 18, 2015
pbtree.R Initial commit Aug 18, 2015
pgls.Ives.R Initial commit Aug 18, 2015
phenogram.R phenogram to return matrix of tip label coordinates Feb 6, 2016
phyl.RMA.R S3 plot method for phyl.RMA object Dec 29, 2016
phyl.cca.R Initial commit Aug 18, 2015
phyl.pairedttest.R Initial commit Aug 18, 2015
phyl.pca.R update to phyl.pca for m>(n-1) Aug 5, 2016
phyl.resid.R Initial commit Aug 18, 2015
phylANOVA.R Initial commit Aug 18, 2015
phylo.heatmap.R phylo.heatmap to deal with NA; option to turn off points in phylogram Feb 4, 2016
phylo.to.map.R updates to phylo.to.map Jul 15, 2016
phylomorphospace.R update to permit nodelabels & tiplabels with phylomorphospace Aug 20, 2015
phylomorphospace3d.R fix ftype option in static method Dec 25, 2016
phylosig.R Initial commit Aug 18, 2015
plotBranchbyTrait.R small update to plotBranchbyTrait to allow palette to be specified as… Dec 7, 2016
plotSimmap.R plot edges originating from the root as a single segmented line Nov 18, 2016
plotTree.wBars.R update to formula method to plotTree.boxplot Jul 25, 2016
ratebystate.R Initial commit Aug 18, 2015
rateshift.R likelihood surface plotter for rateshift method Aug 16, 2016
read.newick.R small fix to read.newick Jan 15, 2016
read.simmap.R Initial commit Aug 18, 2015
rerootingMethod.R fixed bug in rerootingMethod for matrix input Nov 13, 2015
resolveNodes.R new function to perform all possible rotations around a polytomous node Aug 9, 2016
roundPhylogram.R update to roundPhylogram and ls.consensus Jun 11, 2016
sim.corrs.R Initial commit Aug 18, 2015
sim.history.R fix/update to sim.history for setting anc May 11, 2016
sim.rates.R Initial commit Aug 18, 2015
skewers.R Initial commit Aug 18, 2015
splitplotTree.R Initial commit Aug 18, 2015
starTree.R Initial commit Aug 18, 2015
strahlerNumber.R Initial commit Aug 18, 2015
threshBayes.R Initial commit Aug 18, 2015
treeSlice.R Initial commit Aug 18, 2015
utilities.R tiny fix to updated findMRCA Dec 28, 2016
write.simmap.R simplification of untangle & small update to write.simmap Sep 11, 2015
writeAncestors.R Initial commit Aug 18, 2015
writeNexus.R Initial commit Aug 18, 2015