phyloTop: Calculating Topological Properties of Phylogenies

phyloTop provides tools for calculating and viewing topological properties of phylogenetic trees.

Installing phyloTop

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")

Content overview

The key functions available in phyloTop are:

Tree statistics and topological properties:

• 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

Tree visualisation tools:

• 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)

Simulating an epidemic and creating the corresponding genealogy:

• makeEpiRecord: simulate an epidemiological record of infectors, infectees, infection times and recovery times

• getLabGenealogy: create a genealogy from an epidemiological record

Examples

Tree statistics:

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

Tree visualisation tools:

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: