Statistical Exploration of Landscapes of Phylogenetic Trees

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Documentation for package ‘treespace’ version 1.1.4.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

.render.server.info	Auxiliary functions
DengueBEASTMCC	Dengue fever BEAST MCC tree
DengueSeqs	Dengue fever sequences
DengueTrees	BEAST analysis of Dengue fever
findGroves	Identify clusters of similar trees
findMRCIs	Find MRCIs
fluTrees	BEAST analysis of seasonal influenza (A/H3N2)
linearMrca	Linear MRCA function
makeCollapsedTree	Collapse a tree into a single tip per category
medTree	Geometric median tree function
multiDist	Metric function for 'multiPhylo' input
plotGroves	Scatterplot of groups of trees
plotGrovesD3	Scatterplot of groups of trees using 'scatterD3'
plotTreeDiff	Plot tree differences
refTreeDist	Metric function for comparing a reference 'phylo' to 'multiPhylo' input
relatedTreeDist	Tree distance when trees have "related" tips
simulateIndTree	Simulate randomised "individuals" tree
tipDiff	Find tip position differences
tipsMRCAdepths	Tip-tip MRCA depths
treeConcordance	Tree concordance
treeDist	Metric function
treespace	Phylogenetic tree exploration
treespaceServer	Web-based tree explorer
treeVec	Tree vector function
wiwMedTree	Median transmission tree
wiwTreeDist	Transmission tree distance
woodmiceTrees	Bootstrap trees from woodmouse dataset