shade_np: Non-phylogenetic Core Community Using the Shade & Stopnisek...

In holobiont: Microbiome Analysis Tools

Non-phylogenetic Core Community Using the Shade & Stopnisek (2019) algorithm.

Description

Called internally. Identifies all taxa and core taxa of the core community using a non-phylogenetic approach with a modified Shade and Stopnisek (2019) algorithm.

Usage

shade_np(xv, mxtx,fi)

Arguments

xv	(Required) The phyloseq object passed from main functions and containing microbial community data.
mxtx	(Required) The maximum number of branches to add sequentially, as a percentage of the total branches.
fi	(Required) The threshold for the percent increase in beta diversity used to identify the taxon at which point adding more taxa yields diminishing returns in explanatory power.

Details

shade_np is used internally in the holobiont package to identify core edges of a microbial phylogeny for the non-phylogenetic approach using a modified Shade and Stopnisek (2019) algorithm. Briefly, taxa are ranked according to abundance first and then occupancy (i.e., occupancy is more important). Next, taxa are added sequentially, up to a maximum number of taxa. Each time a new taxon is added, the mean beta-diversity (Jaccard) between each pair of samples is calculated and is then averaged across all samples. Next, total beta-diversity (all taxa) between pairs samples is calculated, and again averaged across all samples. Finally, the percent increase in total beta-diversity is calculated for each new taxon added. A threshold is then selected based on the lowest ranked taxon that yields a minimum percent increase in beta-diversity.

Value

This function returns a list of all taxa and core taxa.

References

Shade, Ashley, and Nejc Stopnisek. "Abundance-occupancy distributions to prioritize plant core microbiome membership." Current opinion in microbiology 49 (2019): 50-58.

Examples

#Test with enterotype dataset
library(phyloseq)
library(ape)
library(phytools)
data(enterotype)

set.seed(1)

enterotype<-prune_taxa(taxa_names(enterotype)[2:21],enterotype)
enterotype<-prune_samples(sample_names(enterotype)[2:21],enterotype)

#Generate an example tree and label it with the names of the microbial taxa
enterotype_tree<-rtree(length(taxa_names(enterotype)))
enterotype_tree$tip.label<-taxa_names(enterotype)
enterotype_tree$node.label<-as.character(1:1:enterotype_tree$Nnode)

#Create a phyloseq object with a tree
example_phyloseq<-phyloseq(otu_table(enterotype),phy_tree(as.phylo(enterotype_tree)))
newtree<-bind.tip(phy_tree(example_phyloseq),tip.label='outgroup',edge.length=0.0001,position=0)

shade_np(example_phyloseq, NULL, 2)

holobiont documentation built on Aug. 8, 2025, 7:31 p.m.