Tools for calculating and viewing topological properties of phylogenetic trees.
phyloTop provides tools for calculating and viewing topological properties of phylogenetic trees.
To install the development version from github:
library(devtools)install_github("michellekendall/phyloTop")
The stable version can be installed from CRAN using:
install.packages("phyloTop")
Then, to load the package, use:
library("phyloTop")
The key functions available in phyloTop are:
avgLadder
: find the average ladder size in a tree
cherries
: find the number of cherries in a tree
colless.phylo
: find the Colless imbalance number of a tree
getDepths
: find the depth of each node in a tree
ILnumber
: find the number of nodes with exactly one tip child
ladderSizes
: find the size of any "ladders" in a tree (consecutive nodes, each with exactly one tip child)
maxHeight
: find the maximum height (equivalently, depth) of nodes in a tree
nConfig
: find the sizes of all configurations (equivalently, clades) in a tree
nodeDepth
: find the depth of a given node in a tree
nodeDepthFrac
: find the fraction of nodes in a tree at a given depth
nodeImb
: find the imbalance of a given node in a tree
nodeImbFrac
: find the fraction of nodes in a tree with an imbalance of a given threshold or more
phyloTop
: find a range of tree statistics for a list of trees (faster than calling each function individually)
pitchforks
: find the number of pitchforks (clades of size three) in a tree
sackin.phylo
: find the Sackin index of a tree
splitTop
: find the split topology of a tree - the size of clades at a given depth
stairs
: find the "staircase-ness" measures, as defined by Norstrom et al. 2012
treeImb
: find the tree imbalance - the imbalance at each node
widths
: find the number of nodes at each depth in a tree
configShow
: plot a tree, highlighting the configurations of a given size
ladderShow
: plot a tree, highlighting the "ladders"
subtreeShow
: plot a tree, highlighting the subtree(s) descending from the given node(s)
makeEpiRecord
: simulate an epidemiological record of infectors, infectees, infection times and recovery times
getLabGenealogy
: create a genealogy from an epidemiological record
Apply tree statistic functions to a list of 10 random trees, each with 50 tips:
phyloTop(rmtree(10,50))
Example output:
## avgLadder cherries colless.phylo ILnumber maxHeight pitchforks sackin.phylo stairs1 stairs2## 1 3.000000 19 0.11139456 12 10 8 295 0.7755102 0.01576994## 2 3.000000 12 0.13945578 26 11 7 308 0.6734694 0.01982611## 3 2.000000 19 0.10289116 12 10 7 289 0.5918367 0.01719111## 4 2.750000 17 0.08758503 16 9 6 277 0.5714286 0.01921548## 5 3.000000 19 0.06207483 12 8 7 257 0.4489796 0.02279353## 6 2.666667 16 0.19132653 18 13 8 365 0.3877551 0.01828405## 7 2.000000 18 0.12414966 14 11 8 306 0.9591837 0.01403966## 8 3.000000 18 0.08758503 14 11 9 271 0.4285714 0.02308904## 9 2.500000 14 0.15051020 22 11 11 341 0.9795918 0.01062925## 10 2.000000 17 0.14370748 16 12 8 321 0.2244898 0.02706817
Plot a random tree with 20 tips, highlighting the the clade(s) descending from nodes 23 and 35:
subtreeShow(rtree(20),nodeList=c(23,35), mainCol="navy", subtreeCol="cyan", nodeLabelCol="cyan", edge.width=2)
Example output:
We are very grateful to Leonid Chindelevitch for his comments which have led to this significantly improved version of phyloTop: most of the functions are now calculated in linear time and We have fixed errors in the calculation of the sackin and stairs measures.
phyloTop v1.1.1 was archived on CRAN on 2015-10-29 as it was no longer maintained by its creator, Michael Boyd.
The package has been revived by Michelle Kendall and Caroline Colijn. All of the functions in version 2.0.0 have been updated, with faster implementations, simplified format requirements and dependencies, and further help files and examples added. We have included explanations in the help files wherever version 2.0.0 is not backwards compatible, and documented the deprecated functions.
Major updates include:
all functions accept trees of class phylo or phylo4, automatically changing them to class phylo and coercing them into binary, rooted trees wherever possible.
the functions nConfig, ladderSizes and getDepths (on which many of the others depend) have been freshly implemented and are significantly faster.
the new function phyloTop takes a list of trees and applies a variety of topological functions, returning a matrix of topological statistics (faster than calling each function individually). Other new functions are: makeEpiRecord, nodeImbFrac, nodeDepthFrac, phyloCheck.
many minor functions were only called by one main function - these have been deprecated and subsumed into the code for the main function. Some minor functions are unnecessary now that compuations are performed on trees in phylo rather than phylo4 format - these have been deprecated. Others have been updated and marked as internal.
the functions avgLadder, cherries, ILnumber, maxHeight, pitchforks, and sackin.phylo now contain normalisation options. We thank Giacomo Plazzotta for enabling this by providing their maximum values.
errors arising from submitting a tree with two tips have now been removed. We thank Scott Ward for spotting this problem and supplying code fixes.
further plotting options have been added to the tree visualisation functions configShow, ladderShow and subtreeShow.