FourHcentroid: Centroid of bootstrapped 4H-indices

In HybridMicrobiomes: Analysis of Host-Associated Microbiomes from Hybrid Organisms

Centroid of bootstrapped 4H-indices

Description

Calculates the centroid of a set of 4H-indices from bootstrapped samples.

Usage

FourHcentroid(boots)

Arguments

boots

(Required) Output matrix from the FourHbootstrap function

Details

FourHcentroid averages over each column of the output matrix from FourHbootstrap and prints out the average value of each dimension (\mathcal{U}, \mathcal{I}, \mathcal{G}, \mathcal{L}) of the 4H-index. It also calculates and prints out the average value for \sigma.

Value

This function outputs a dataframe reporting the average values of each dimension of the 4H-index, and the average value of \sigma.

Examples

#Test with enterotype dataset
library(phyloseq)
data(enterotype)
#Covert the OTU table to reads, rather than fractional abundances
otu_table(enterotype)<-round(10000*otu_table(enterotype))

#Randomly assign host classes (these should be known in a real hybrid microbiome dataset)
#The two parent species are assigned '1' and '3' respectively, the hybrid is assigned '2'
hybrid_status<-sample(1:3,280, replace=TRUE)

#Bootstrap the dataset
boot_samples<-FourHbootstrap(enterotype,hybrid_status,0.5,5,10)

#Find the centroid of the bootstrap samples
FourHcentroid(boot_samples)

HybridMicrobiomes documentation built on May 29, 2024, 2:15 a.m.