BootA {shipunov} | R Documentation |
Bootstrap clustering
Description
How to bootstrap clustering with 'ape'
Usage
BootA(dat, FUN=function(.x) ape::nj(dist(.x)), iter=1000, mc.cores=1, tresh=50,
cons=TRUE, prop=0.5)
Arguments
dat |
data |
FUN |
how to bootstrap (see examples) |
iter |
number of iterations, default 1000 |
mc.cores |
how many cores to employ (system-dependent) |
tresh |
Threshold for printing bootstrap values |
cons |
Calculate consensus tree? |
prop |
0.5 is majority-rule consensus (default), 1 is strict consensus |
Details
This is how to bootstrap clustering with 'ape::boot.phylo()'.
Author(s)
Alexey Shipunov
See Also
Bclust
, BootA
, ape::boot.phylo
Examples
dat <- iris[, -5]
row.names(dat) <- abbreviate(make.names(iris[, 5], unique=TRUE))
iris.BA1 <- BootA(dat, iter=100)
plot(iris.BA1$boot.tree, show.node.label=TRUE)
plot(iris.BA1$cons.tree)
iris.BA2 <- BootA(dat, FUN=function(.x) ape::as.phylo(hclust(dist(.x))), iter=100)
## Not run:
## change (or remove) 'mc.cores=...' in accordance with your system features
iris.BA3 <- BootA(dat, FUN=function(.x) phangorn::NJ(dist(.x)), iter=100,
mc.cores=4)
## End(Not run)
[Package shipunov version 1.17.1 Index]