treestructure

Citation

E.M. Volz, Wiuf, C., Grad, Y., Frost, S., Dennis, A., Didelot, X.D. (2020) Identification of hidden population structure in time-scaled phylogenies. Systematic Biology. https://doi.org/10.1101/704528

Installation

To install latest development version, first install the devtools package and then from your R console run:

devtools::install_github( 'emvolz-phylodynamics/treestructure' )

Alternatively, download this repository and follow instructions for your OS on installing packages from source.

A command-line interface is available. See inst/tscl.

Quick start

This example shows trestruct applied to a simulated structured coalescent tree that includes samples from a large constant size population and samples from three small 'outbreaks' which are growing exponentially.

library(treestructure)

## Loading required package: ape

( tree <- read.tree( system.file('sim.nwk', package='treestructure') ) ) 

## 
## Phylogenetic tree with 275 tips and 274 internal nodes.
## 
## Tip labels:
## 	1, 1, 1, 1, 1, 1, ...
## 
## Rooted; includes branch lengths.

s <- trestruct( tree ) 

## Finding splits under nodes: 276 
## Finding splits under nodes: 276 280 
## Finding splits under nodes: 276 447 
## Finding splits under nodes: 276 498

You can print the results:

print(s) 

## Call: 
## trestruct(tre = tree)
## 
## Number of clusters: 4 
## Number of partitions: 2 
## Significance level: 0.01 
## Cluster and partition assignment: 
##    taxon cluster partition
## 1      1       1         1
## 2      1       1         1
## 3      1       1         1
## 4      1       1         1
## 5      1       1         1
## 6      1       1         1
## 7      1       1         1
## 8      1       1         1
## 9      1       1         1
## 10     1       1         1
## ...
## For complete data, use `as.data.frame(...)` 
## 

The default plotting behavior uses the ggtree package if available.

plot(s)  + ggtree::geom_tiplab() 

If not, or if desired, ape plots are available

plot( s, use_ggtree = FALSE )