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Compute the mean for each taxa across population

compute_mean_microbiome.Rd

This function estimate the mean microbiome by averaging abundances across individuals for each taxa. Optionally, it use a Dirichlet distribution to simulate inter-individual variability centered arround the mean.

Usage

compute_mean_microbiome(microbiome, dir = F, n_ind = NULL, ao, mix.params)

Arguments

microbiome

A matrix of microbiome abundances (taxa in rows, individuals in columns).

dir

A logical; if TRUE, use a Dirichlet distribution to simulate inter-individual variability. Default is FALSE.

n_ind

The number of individuals to simulate with the Dirichlet distribution (required if dir = TRUE).

ao

A numeric scalar used as the concentration parameter for the Dirichlet distribution.

mix.params

A numeric vector (length = 2) specifying weights between Dirichlet samples and the original mean. The weigths should sum to 1.

Value

A numericvector of mean microbiome values if dir = FALSE. A matrix of simulated microbiomes if dir = TRUE

See also

compute_current_microbiome()