holobiont (version 0.1.3)

basic_tip: Tip-based Core Community Phylogeny Using Thresholds

Description

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

Usage

basic_tip(xv, nt, cf, abt1, abt2, abt3,rt)

Value

This function returns a list of all edges and core edges, as well as all taxa and core taxa.

Arguments

xv

(Required) The phyloseq object passed from main functions and containing microbial community data.

nt

(Required) The microbial phylogeny passed from main functions.

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.

rt

Whether to include the root of the phylogeny. The default is TRUE, meaning that the root is necessarily included in all phylogenies. This requires that the input tree be rooted.

Details

basic_tip is used internally in the holobiont package to identify core edges of a microbial phylogeny for the tip-based approach using thresholds.

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_tip(example_phyloseq, phy_tree(example_phyloseq), 0.5, 0, 0, 0,TRUE)