inst/doc/structuredCoalescent.R

In treestructure: Detect Population Structure Within Phylogenetic Trees

## ----setup, include = FALSE----------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width=7,
  fig.height=11
)

## ----message=FALSE-------------------------------------------------------
library(treestructure)

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

## ----message=FALSE-------------------------------------------------------
s <- trestruct( tree ) 

## ------------------------------------------------------------------------
print(s) 

## ----message=FALSE-------------------------------------------------------
plot(s)  + ggtree::geom_tiplab() 

## ------------------------------------------------------------------------
plot( s, use_ggtree = FALSE )

## ------------------------------------------------------------------------
structureData <- as.data.frame( s ) 
head( structureData )

## ------------------------------------------------------------------------
with ( structureData, 
	ape::keep.tip(s$tree,  taxon[ partition==1 ] ) 
) -> partition1
partition1
plot(partition1)

## ----message=FALSE-------------------------------------------------------
trestruct( tree, level = .05, minCladeSize = 5 )