coreFaithsPD: Faiths PD of the Core Microbiome

In holobiont: Microbiome Analysis Tools

Faiths PD of the Core Microbiome

Description

Calculates Faith's phylogenetic diversity (PD) of a core microbiome based on either the tip-based or the branch-based core community phylogeny.

Usage

coreFaithsPD(x, core_fraction = 0.5, ab_threshold1 = 0,
ab_threshold2 = 0, ab_threshold3 = 0, mode='branch',
selection='basic', max_tax = NULL, increase_cutoff = 2,
initial_branches = NULL, rooted=TRUE)

Arguments

x	(Required) Microbial community data. This must be in the form of a phyloseq object and must contain, at a minimum, an OTU abundance table and a phylogeny.
core_fraction	The fraction of samples that a microbial taxon must be found in to be considered part of the 'core' microbiome. This variable is only used when selection = 'basic' and is ignored when selection = 'shade'. The default value is 0.5.
ab_threshold1	The threshold for mean relative abundance across all samples. This variable is only used when selection = 'basic' and is ignored when selection = 'shade'. The default value is 0.
ab_threshold2	The threshold for maximum relative abundance in any sample. This variable is only used when selection = 'basic' and is ignored when selection = 'shade'. The default value is 0.
ab_threshold3	The threshold for minimum relative abundance across all samples. This variable is only used when selection = 'basic' and is ignored when selection = 'shade'. The default value is 0.
mode	Whether to build a tip-based ('tip') or a branch-based ('branch') phylogeny. The default is 'branch'.
selection	Whether to use thresholds ('basic') or the Shade and Stopnisek method ('shade') to define the core community. The default is 'basic'.
max_tax	The maximum number of branches to add sequentially, as a percentage of the total branches when using the Shade and Stopnisek method. This variable is only used when selection = 'shade' and is ignored when selection = 'basic'.
increase_cutoff	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. This variable is only used when selection = 'shade' and is ignored when selection = 'basic'.
initial_branches	The number of branches to include prior to testing for increases in beta diversity. The default is to use all branches that are present in every sample and to begin testing branches that are missing from at least one sample. This variable is only used when selection = 'shade' and is ignored when selection = 'basic'.
rooted	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

coreFaithsPD calculates Faith's PD (Faith, 1992) based on either the tip-based or the branch-based core community phylogeny using either basic thresholds or a modification of the Shade and Stopnisek (2019) algorithm. In both cases, Faith's PD is calculated as the sum of the branch lengths in the core community phylogeny. For more details, see Bewick and Camper (2025).

Value

This function returns the numeric value of Faith's PD for the core microbiome.

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)

#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)))

coreFaithsPD(example_phyloseq)

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