test.biotypes: Robustness of enterotypes clusters

In tapj/biotyper: BiotypeR: an R package to biotype a community

Description

To assess whether the samples are continuously distributed in the phylogenetic composition space, or whether they predominantly congregate around a few cluster centers

Usage

test.biotypes(biotyper.obj, biotyper.obj.simul)

## S3 method for class 'biotypes.test'
print(biotypes.test)
## S3 method for class 'biotypes.test'
plot(biotypes.test)

Arguments

biotyper.obj	an object of class "biotyper.obj", i.e. a biotyper object
biotyper.obj.simul	an object of class "biotyper.obj.simul", i.e. a biotyper object from simulated data
biotypes.test	a biotypes.test object from test.biotypes

Value

A list of element :

silhouette.test	p.values according uniform, normal, log.normal distribution
silhouette.simul	Silhouette simulated coef. according uniform, normal, log.normal distribution simulation
observed.sil	Observed silhouette coef. from biotyper.obj

Author(s)

Julien Tap

Examples

## Not run: 
## Not run:
data(Titanium16S)
Titanium.jsd=dist.JSD(Titanium16S)
ch=CH.index(Titanium16S.jsd)
k=which(ch==max(ch))

ecosimulation=ecosimulator(Titanium16S, 100)
biotyper.obj.simul=biotyper(ecosimulation, k)


biotyper.obj=biotyper(Titanium16S, k, distance.jsd=Titanium16S.jsd)

test=test.biotypes(biotyper.obj, biotyper.obj.simul)
plot(test)

## End (Not run)

## End(Not run)

tapj/biotyper documentation built on Oct. 23, 2021, 5:44 a.m.