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In ecodive: Parallel and Memory-Efficient Ecological Diversity Metrics

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Description

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Arguments

alpha	How much weight to give to relative abundances; a value between 0 and 1, inclusive. Setting alpha=1 is equivalent to normalized_unifrac().
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').
cpus	How many parallel processing threads should be used. The default, n_cpus(), will use all logical CPU cores.
cutoff	The maximum number of observations to consider "rare". Default: 10.
digits	Precision of the returned values, in number of decimal places. E.g. the default digits=3 could return 6.392.
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.
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.
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.
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
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').

ecodive documentation built on Jan. 16, 2026, 5:11 p.m.