In MichelleKendall/phyloTop: Calculating Topological Properties of Phylogenies

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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:

set.seed(123)
phyloTop(rmtree(10,50))

Tree visualisation tools:

Plot a random tree with 20 tips, highlighting the the clade(s) descending from nodes 25 and 33:

subtreeShow(rtree(20),nodeList=c(25,33), mainCol="navy", subtreeCol="cyan", nodeLabelCol="cyan", edge.width=2)

Contributing / asking a question

Contributions are welcome via pull requests.

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Questions, feature requests and bugs can be reported using the package's issue system.

MichelleKendall/phyloTop documentation built on Feb. 1, 2023, 8:07 a.m.