SPIEC-EASI matrix (Rcpp implementation) — spieceasi_matrix

Fast C++-accelerated SPIEC-EASI. Uses Rcpp for CLR transformation; Uses huge for estimation and huge.select for StARS model selection. Input: samples x taxa matrix.

Usage

spieceasi_matrix_rcpp(
  data,
  method = "glasso",
  output = c("partial_correlation", "adjacency", "covariance", "correlation",
    "precision", "beta", "stability"),
  ...
)

Arguments

data: Numeric matrix. Rows = samples, columns = taxa (ASVs/OTUs).
method: Character. "glasso" or "mb".
output: Character. One of "partial_correlation", "adjacency", "covariance", "correlation", "precision", "beta", "stability".
...: Passed to spieceasi_fit_rcpp (e.g. pulsar.select, pulsar.params or stars.params, verbose).

Value

Matrix as requested by output.

Examples

if (FALSE) { # \dontrun{
pcor_mat <- spieceasi_matrix_rcpp(asv_mat, method = "glasso", output = "partial_correlation")
adj_mat  <- spieceasi_matrix_rcpp(asv_mat, method = "glasso", output = "adjacency")
} # }