faith: Faith's PD

In ecodive: Parallel and Memory-Efficient Ecological Diversity Metrics

Faith's PD

Description

Faith's phylogenetic diversity metric.

A higher value indicates a greater amount of evolutionary history represented within the community, suggesting higher biodiversity in terms of evolutionary relationships.

Usage

faith(counts, tree = NULL, cpus = n_cpus())

Arguments

counts	An OTU abundance matrix where each column is a sample, and each row is an OTU. Any object coercible with as.matrix() can be given here, as well as phyloseq, rbiom, SummarizedExperiment, and TreeSummarizedExperiment objects.
tree	A phylo-class object representing the phylogenetic tree for the OTUs in counts. The OTU identifiers given by colnames(counts) must be present in tree. Can be omitted if a tree is embedded with the counts object or as attr(counts, 'tree').
cpus	How many parallel processing threads should be used. The default, n_cpus(), will use all logical CPU cores.

Value

A numeric vector.

Calculation

Given n branches with lengths L and a sample's abundances on each of those branches coded as 1 for present or 0 for absent:

\sum_{i = 1}^{n} P_i \times L_i

References

Faith DP 1992. Conservation evaluation and phylogenetic diversity. Biological Conservation, 61:1-10. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/0006-3207(92)91201-3")}

See Also

Other alpha_diversity: chao1(), inv_simpson(), shannon(), simpson()

Examples

    # Example counts matrix
    ex_counts
    
    # Faith diversity values
    faith(ex_counts, tree = ex_tree)
    

ecodive documentation built on Aug. 23, 2025, 1:13 a.m.