% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/nmfae.signed.R
\name{nmfae.signed.inference}
\alias{nmfae.signed.inference}
\title{Statistical Inference for Signed-Bottleneck NMF-AE Signed Bottleneck}
\usage{
nmfae.signed.inference(object, Y1, Y2 = Y1, wild.bootstrap = TRUE, ...)
}
\arguments{
\item{object}{A fitted \code{"nmfae.signed"} object.}

\item{Y1}{Output matrix used during fitting.}

\item{Y2}{Input matrix used during fitting.  Default \code{Y1}.}

\item{wild.bootstrap}{Logical.  Default \code{TRUE}.}

\item{...}{Additional arguments:
\describe{
\item{\code{wild.B}}{Bootstrap replicates.  Default 500.}
\item{\code{wild.seed}}{RNG seed.  Default 123.}
\item{\code{wild.level}}{CI confidence level.  Default 0.95.}
\item{\code{sandwich}}{Use sandwich covariance.  Default \code{TRUE}.}
\item{\code{C.p.side}}{P-value type: \code{"two.sided"} (default for
Signed-Bottleneck NMF-AE) or \code{"one.sided"}.}
\item{\code{cov.ridge}}{Ridge stabilization.  Default \code{1e-8}.}
\item{\code{print.trace}}{Logical.  Default \code{FALSE}.}
}}
}
\value{
An object of class \code{c("nmfae.signed.inference",
  "nmfae.inference", "nmfae.signed", "nmfae", "nmf")} with added fields:
\item{sigma2.used}{Estimated \eqn{\sigma^2}.}
\item{C.se, C.se.boot}{Sandwich / bootstrap SEs for \eqn{\Theta} (Q x R).}
\item{C.ci.lower, C.ci.upper}{Bootstrap CIs.}
\item{coefficients}{Data frame with Estimate, SE, BSE, z, p-value, CI.}
\item{C.p.side}{P-value side used.}
}
\description{
Post-estimation inference for the \strong{signed} bottleneck
\eqn{\Theta = C_{+} - C_{-}} in the Signed-Bottleneck NMF-AE model
\eqn{Y_1 \approx X_1 \Theta X_2 Y_2}, conditional on
\eqn{(\hat X_1, \hat X_2)}.  Uses sandwich covariance and wild bootstrap
\strong{without} the non-negativity projection that \code{\link{nmfae.inference}}
applies (because \eqn{\Theta} is unconstrained in sign here).
}
\section{Lifecycle}{

This function is \strong{experimental}. The interface may change in
future versions.
}

\references{
Ding, C. H. Q., Li, T., & Jordan, M. I. (2010). Convex and
semi-nonnegative matrix factorizations. \emph{IEEE Transactions on
Pattern Analysis and Machine Intelligence}, 32(1), 45--55.
}
\seealso{
\code{\link{nmfae.signed}}, \code{\link{nmfae.inference}}
}
