Compute microbiomes for all individuals of current generation gathering all relevant object already computed.

Compute microbiomes for all individuals of current generation gathering all relevant object already computed.

Usage

compute_current_microbiome(
  beta,
  current_genotypes,
  mother_microbiomes,
  mean_microbiome,
  noise = 0.1,
  taxa_scale,
  lambda = 0.5,
  dir = F,
  thetaX
)

Arguments

beta

A matrix of taxa (rows) by SNPs (columns) representing the multiplicative effect of SNPs on taxa abundances. Typically the output of compute_beta_matrix_cluster()

current_genotypes

A matrix of genotypes for the individuals of the current generation.

mother_microbiomes

A matrix containing the CLR-transformed abundances from the microbiome of the current mothers.

mean_microbiome

A numeric vector representing the average abundances of the microbiome within the population.

noise

A numeric scalar indicating the standard deviation of the Gaussian noise to add during beta g construction compute_beta_g()(multiplicative genetic effect on taxa abundances).

taxa_scale

A numeric scalar to scale the noise added to each OTUs abundance, see compute_beta_g().

lambda

A numeric between 0 and 1 controlling the relative contribution of the mother microbiome compared to the average microbiome.

dir

A logical;

thetaX

A matrix representing the environmental effect (optional).

Value

A matrix of CLR-transformed abundances of the microbiome for each individual of the current generation.

See also

compute_mean_microbiome()