R/network_cov_parallel.R

In sysbiomed/glmSparseNet: Network Centrality Metrics for Elastic-Net Regularized Models

#' Calculates the covariance network
#'
#' @inheritParams networkCorParallel
#'
#' @return depends on build.output parameter
#' @export
#'
#' @examples
#' n.col <- 6
#' xdata <- matrix(rnorm(n.col * 4), ncol = n.col)
#' networkCovParallel(xdata)
networkCovParallel <- function(xdata,
                               buildOutput = "matrix",
                               nCores = 1,
                               forceRecalcNetwork = FALSE,
                               showMessage = FALSE,
                               ...,
                               # Deprecated arguments with dots in name
                               # nolint start: object_name_linter.
                               build.output = deprecated(),
                               n.cores = deprecated(),
                               force.recalc.network = deprecated(),
                               show.message = deprecated()) {
    # nolint end: object_name_linter.
    # Lifecycle management: to remove after 1.23.0
    if (lifecycle::is_present(build.output)) {
        .deprecatedDotParam("networkCovParallel", "build.output")
        buildOutput <- build.output
    }
    if (lifecycle::is_present(n.cores)) {
        .deprecatedDotParam("networkCovParallel", "n.cores")
        nCores <- n.cores
    }
    if (lifecycle::is_present(force.recalc.network)) {
        .deprecatedDotParam("networkCovParallel", "force.recalc.network")
        forceRecalcNetwork <- force.recalc.network
    }
    if (lifecycle::is_present(show.message)) {
        .deprecatedDotParam("networkCovParallel", "show.message")
        showMessage <- show.message
    }
    # Lifecycle management: end

    .networkGenericParallel(
        stats::cov,
        "covariance",
        xdata,
        buildOutput = buildOutput,
        nCores = nCores,
        forceRecalcNetwork = forceRecalcNetwork,
        showMessage = showMessage,
        ...
    )
}