phyloseq_phylo_div: Estimate phylogenetic diversity (PD), mean pairwise distance...

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Estimate phylogenetic diversity (PD), mean pairwise distance (MPD), and mean nearest taxon distance (MNTD).

Description

Currently only non-abundance-weighted estimates are implemented.

Usage

phyloseq_phylo_div(
  physeq,
  measures = c("PD", "MPD", "MNTD", "SES.PD", "SES.MPD", "SES.MNTD"),
  ...
)

Arguments

physeq	A phyloseq-class object (phylogenetic tree is required)
measures	Character vector with diversity indices names ("PD", "MPD", "MNTD", "SES.PD", "SES.MPD", "SES.MNTD")
...	Additional arguments (standardize, null.model, abundance.weights) may be passed to pd.query

Details

Implementation of the phylogenetic diversity measures is based on the PhyloMeasures package which is much faster than corresponding functions from picante package.

MNTD index sometimes is also reffered as MNND (mean nearest neighbour distance).

Diversity values could be standardized to the mean and expectation of the metric (SES, standardized effect size) by passing additional argument ('standardize = T') to the function or directly calling esimation of this measures ('measures = c("SES.PD", "SES.MPD", "SES.MNTD")'). Standardization leads to some of the most commonly used measures, including NRI (net relatedness index, the standardized version of MPD), NTI (nearest taxon index, derived from MNTD) and PDI (phylogenetic diversity index, derived from PD). These metrics describe how diffrent the observed species assemblages is from other possible assemblages of the same size. With this standardization, values of 0 are consistent with random phylogenetic structure, while phylogenetic clustering is associated with negative values, and phylogenetic overdispersion with positive values. The default null model preserves only the species richness of samples (abundance is not maintained), which leads to the taxon shuff approach ("taxa.labels" null model from picante). Note that standardization is performed by evaluating analytical expressions for the mean and variance of the basic measures, rather than by the slow and inexact randomization techniques (as in phyloseq_phylo_ses).

Value

A data.frame of the diversity estimates.

References

Tsirogiannis C., Sandel B. (2016) PhyloMeasures: a package for computing phylogenetic biodiversity measures and their statistical moments. Ecography, 39, 709–714. doi:10.1111/ecog.01814

Webb C., Ackerly D., McPeek M., and Donoghue M. (2002) Phylogenies and community ecology. Annual Review of Ecology and Systematics, 33, 475-505.

Faith D.P. (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10.

See Also

phyloseq_phylo_ses, mpd.query, mntd.query, and pd.query from PhyloMeasures package; mpd, mntd, and pd from picante package; estimate_richness, phy_tree

Examples

# Load data
data(esophagus)

# Estimate phylogenetic diversity (PD) and mean pairwise phylogenetic distance (MPD)
phyloseq_phylo_div(esophagus, measures = c("PD", "MPD"))

# Standardized effect size of phylogenetic diversity (PDI)
phyloseq_phylo_div(esophagus, measures = "PD", standardize = T)
phyloseq_phylo_div(esophagus, measures = "SES.PD")  # the same

vmikk/metagMisc documentation built on Feb. 14, 2024, 2:29 a.m.