basic_np: Non-phylogenetic Core Community Phylogeny Using Thresholds

In holobiont: Microbiome Analysis Tools

Non-phylogenetic Core Community Phylogeny Using Thresholds

Description

Called internally. Identifies all edges and core edges of the core community phylogeny using a non-phylogenetic approach with core thresholds.

Usage

basic_np(xv, cf, abt1, abt2, abt3)

Arguments

xv	(Required) The phyloseq object passed from main functions and containing microbial community data.
cf	(Required) The fraction of samples that a microbial taxon must be found in to be considered part of the 'core' microbiome.
abt1	(Required) The threshold for mean abundance across all samples.
abt2	(Required) The threshold for maximum abundance in any sample.
abt3	(Required) The threshold for the minimum abundance across all samples.

Details

basic_np is used internally in the holobiont package to identify all taxa and all core taxa for the non-phylogenetic approach using thresholds.

Value

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

Examples

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

set.seed(1)

#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)

#Create a phyloseq object with a tree
example_phyloseq<-phyloseq(otu_table(enterotype),phy_tree(as.phylo(enterotype_tree)))

basic_np(example_phyloseq, 0.5, 0, 0, 0)

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