# Statistical Exploration of Landscapes of Phylogenetic Trees

## Documentation for package ‘treespace’ version 1.1.4.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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