treespace1.1.4.3 package

Statistical Exploration of Landscapes of Phylogenetic Trees

dot-render.server.info

Auxiliary functions

findGroves

Identify clusters of similar trees

findMRCIs

Find MRCIs

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 inpu...

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

Download source packageRead PDF manual

Tools for the exploration of distributions of phylogenetic trees. This package includes a 'shiny' interface which can be started from R using treespaceServer(). For further details see Jombart et al. (2017) <DOI:10.1111/1755-0998.12676>.

  • Maintainer: Michelle Kendall
  • License: MIT + file LICENSE
  • Last published: 2023-09-07

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