Nothing
## ----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 )
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