% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/spieceasi_matrix_rcpp.R
\name{spieceasi_matrix_rcpp}
\alias{spieceasi_matrix_rcpp}
\title{SPIEC-EASI matrix (Rcpp implementation)}
\usage{
spieceasi_matrix_rcpp(
  data,
  method = "glasso",
  output = c("partial_correlation", "adjacency", "covariance", "correlation",
    "precision", "beta", "stability"),
  ...
)
}
\arguments{
\item{data}{Numeric matrix. Rows = samples, columns = taxa (ASVs/OTUs).}

\item{method}{Character. "glasso" or "mb".}

\item{output}{Character. One of "partial_correlation", "adjacency", "covariance",
"correlation", "precision", "beta", "stability".}

\item{...}{Passed to \code{spieceasi_fit_rcpp} (e.g. \code{pulsar.select},
\code{pulsar.params} or \code{stars.params}, \code{verbose}).}
}
\value{
Matrix as requested by \code{output}.
}
\description{
Fast C++-accelerated SPIEC-EASI. Uses Rcpp for CLR transformation;
Uses \code{huge} for estimation and \code{huge.select} for StARS model selection. Input: samples x taxa matrix.
}
\examples{
\dontrun{
pcor_mat <- spieceasi_matrix_rcpp(asv_mat, method = "glasso", output = "partial_correlation")
adj_mat  <- spieceasi_matrix_rcpp(asv_mat, method = "glasso", output = "adjacency")
}
}
