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In ecodive: Parallel and Memory-Efficient Ecological Diversity Metrics

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Description

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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.
weighted	If TRUE, the algorithm takes relative abundances into account. If FALSE, only presence/absence is considered.
normalized	For weighted UniFrac only, normalize distances by the total branch length. Options: TRUE or FALSE.
alpha	How much weight to give to relative abundances; a value between 0 and 1, inclusive. Setting alpha=1 is equivalent to weighted_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.
cpus	How many parallel processing threads should be used. The default, n_cpus(), will use all logical CPU cores.

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