phyloTop: Calculating Topological Properties of Phylogenies

Tools for calculating and viewing topological properties of phylogenetic trees.

Author
Michelle Kendall [aut, cre], Michael Boyd [aut], Caroline Colijn [aut]
Date of publication
2016-04-19 08:59:43
Maintainer
Michelle Kendall <m.kendall@imperial.ac.uk>
License
GPL-2
Version
2.0.0

View on CRAN

Man pages

avgLadder
Average ladder size
cherries
Cherry number
colless.phylo
Colless number
configShow
Plot a tree highlighting configurations
getDepths
Find the depth of each node
getLabGenealogy
Create genealogy
ILnumber
IL number
ladderShow
Show ladders
ladderSizes
Ladder sizes
makeEpiRecord
Simulate epidemiological record
makePhyloTree
Make phylogenetic tree (internal)
maxHeight
Maximum tree height
nConfig
Configuration sizes in a tree
nodeDepth
Node depth
nodeDepthFrac
Fraction of nodes beyond a given depth
nodeImb
Node imbalance
nodeImbFrac
Fraction of nodes with given imbalance
phyloCheck
Check tree format (internal)
phyloTop
phyloTop: topological properties of phylogenies
pitchforks
Number of pitchforks
rtree4
Random phylo4 tree
sackin.phylo
Sackin index
splitTop
Split topology
stairs
Stairs
subtreeShow
Highlight a subtree
treeImb
Tree imbalance
widths
Number of nodes at each depth

Files in this package

phyloTop
phyloTop/tests
phyloTop/tests/testthat.R
phyloTop/tests/testthat
phyloTop/tests/testthat/testbasics.R
phyloTop/NAMESPACE
phyloTop/NEWS.md
phyloTop/R
phyloTop/R/phyloTop.R
phyloTop/R/getLabGenealogy.R
phyloTop/R/maxHeight.R
phyloTop/R/subtreeShow.R
phyloTop/R/widths.R
phyloTop/R/configShow.R
phyloTop/R/sackin.R
phyloTop/R/phyloCheck.R
phyloTop/R/avgLadder.R
phyloTop/R/ladderSizes.R
phyloTop/R/rtree4.R
phyloTop/R/splitTop.R
phyloTop/R/stairs.R
phyloTop/R/makeEpiRecord.R
phyloTop/R/nodeImb.R
phyloTop/R/treeImb.R
phyloTop/R/deprecated.R
phyloTop/R/pitchforks.R
phyloTop/R/nodeDepthFrac.R
phyloTop/R/nodeImbFrac.R
phyloTop/R/ladderShow.R
phyloTop/R/cherries.R
phyloTop/R/colless.R
phyloTop/R/nodeDepth.R
phyloTop/R/makePhyloTree.R
phyloTop/R/getDepths.R
phyloTop/R/ILnumber.R
phyloTop/R/nConfig.R
phyloTop/vignettes
phyloTop/vignettes/figs
phyloTop/vignettes/figs/subtreeShowExample.png
phyloTop/README.md
phyloTop/MD5
phyloTop/build
phyloTop/build/partial.rdb
phyloTop/DESCRIPTION
phyloTop/man
phyloTop/man/makeEpiRecord.Rd
phyloTop/man/getLabGenealogy.Rd
phyloTop/man/nodeDepthFrac.Rd
phyloTop/man/maxHeight.Rd
phyloTop/man/pitchforks.Rd
phyloTop/man/sackin.phylo.Rd
phyloTop/man/rtree4.Rd
phyloTop/man/ILnumber.Rd
phyloTop/man/phyloCheck.Rd
phyloTop/man/treeImb.Rd
phyloTop/man/avgLadder.Rd
phyloTop/man/nConfig.Rd
phyloTop/man/makePhyloTree.Rd
phyloTop/man/getDepths.Rd
phyloTop/man/phyloTop.Rd
phyloTop/man/nodeImb.Rd
phyloTop/man/cherries.Rd
phyloTop/man/nodeDepth.Rd
phyloTop/man/splitTop.Rd
phyloTop/man/configShow.Rd
phyloTop/man/stairs.Rd
phyloTop/man/ladderShow.Rd
phyloTop/man/widths.Rd
phyloTop/man/colless.phylo.Rd
phyloTop/man/ladderSizes.Rd
phyloTop/man/nodeImbFrac.Rd
phyloTop/man/subtreeShow.Rd