ecodive (version 2.2.2)

beta_div: Beta Diversity Wrapper Function

Description

Beta Diversity Wrapper Function

Usage

beta_div(
  counts,
  metric,
  norm = "percent",
  power = 1.5,
  pseudocount = NULL,
  alpha = 0.5,
  tree = NULL,
  pairs = NULL,
  margin = 1L,
  cpus = n_cpus()
)

Value

A numeric vector.

Arguments

counts

A numeric matrix of count data where each column is a feature, and each row is a sample. Any object coercible with as.matrix() can be given here, as well as phyloseq, rbiom, SummarizedExperiment, and TreeSummarizedExperiment objects. For optimal performance with very large datasets, see the guide in vignette('performance').

metric

The name of a beta diversity metric. One of c('aitchison', 'bhattacharyya', 'bray', 'canberra', 'chebyshev', 'chord', 'clark', 'divergence', 'euclidean', 'generalized_unifrac', 'gower', 'hamming', 'hellinger', 'horn', 'jaccard', 'jensen', 'jsd', 'lorentzian', 'manhattan', 'matusita', 'minkowski', 'morisita', 'motyka', 'normalized_unifrac', 'ochiai', 'psym_chisq', 'soergel', 'sorensen', 'squared_chisq', 'squared_chord', 'squared_euclidean', 'topsoe', 'unweighted_unifrac', 'variance_adjusted_unifrac', 'wave_hedges', 'weighted_unifrac'). Flexible matching is supported (see below). Programmatic access via list_metrics('beta').

norm

Normalize the incoming counts. Options are:

norm = "percent" -

Relative abundance (sample abundances sum to 1).

norm = "binary" -

Unweighted presence/absence (each count is either 0 or 1).

norm = "clr" -

Centered log ratio.

norm = "none" -

No transformation.

Default: 'percent', which is the expected input for these formulas.

power

Scaling factor for the magnitude of differences between communities (\(p\)). Default: 1.5

pseudocount

The value to add to all counts in counts to prevent taking log(0) for unobserved features. The default, NULL, selects the smallest non-zero value in counts.

alpha

How much weight to give to relative abundances; a value between 0 and 1, inclusive. Setting alpha=1 is equivalent to normalized_unifrac().

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').

pairs

Which combinations of samples should distances be calculated for? The default value (NULL) calculates all-vs-all. Provide a numeric or logical vector specifying positions in the distance matrix to calculate. See examples.

margin

If your samples are in the matrix's rows, set to 1L. If your samples are in columns, set to 2L. Ignored when counts is a phyloseq, rbiom, SummarizedExperiment, or TreeSummarizedExperiment object. Default: 1L

cpus

How many parallel processing threads should be used. The default, n_cpus(), will use all logical CPU cores.

Details

List of Beta Diversity Metrics

Option / Function Name	Metric Name
aitchison	Aitchison distance
bhattacharyya	Bhattacharyya distance
bray	Bray-Curtis dissimilarity
canberra	Canberra distance
chebyshev	Chebyshev distance
chord	Chord distance
clark	Clark's divergence distance
divergence	Divergence
euclidean	Euclidean distance
generalized_unifrac	Generalized UniFrac (GUniFrac)
gower	Gower distance
hamming	Hamming distance
hellinger	Hellinger distance
horn	Horn-Morisita dissimilarity
jaccard	Jaccard distance
jensen	Jensen-Shannon distance
jsd	Jesen-Shannon divergence (JSD)
lorentzian	Lorentzian distance
manhattan	Manhattan distance
matusita	Matusita distance
minkowski	Minkowski distance
morisita	Morisita dissimilarity
motyka	Motyka dissimilarity
normalized_unifrac	Normalized Weighted UniFrac
ochiai	Otsuka-Ochiai dissimilarity
psym_chisq	Probabilistic Symmetric Chi-Squared distance
soergel	Soergel distance
sorensen	Dice-Sorensen dissimilarity
squared_chisq	Squared Chi-Squared distance
squared_chord	Squared Chord distance
squared_euclidean	Squared Euclidean distance
topsoe	Topsoe distance
unweighted_unifrac	Unweighted UniFrac
variance_adjusted_unifrac	Variance-Adjusted Weighted UniFrac (VAW-UniFrac)
wave_hedges	Wave Hedges distance
weighted_unifrac	Weighted UniFrac

Flexible name matching

Case insensitive and partial matching. Any runs of non-alpha characters are converted to underscores. E.g. metric = 'Weighted UniFrac selects weighted_unifrac.

UniFrac names can be shortened to the first letter plus "unifrac". E.g. uunifrac, w_unifrac, or V UniFrac. These also support partial matching.

Finished code should always use the full primary option name to avoid ambiguity with future additions to the metrics list.

Examples

    # Example counts matrix
    ex_counts
    
    # Bray-Curtis distances
    beta_div(ex_counts, 'bray')
    
    # Generalized UniFrac distances
    beta_div(ex_counts, 'GUniFrac', tree = ex_tree)