% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/metabom8-package.R
\docType{package}
\name{metabom8}
\alias{metabom8-package}
\alias{metabom8}
\title{metabom8: A High-Performance R Package for Metabolomics Modeling and Analysis}
\description{
metabom8 (pronounced \emph{metabo-mate}) provides pipelines for 1D NMR data import,
preprocessing, multivariate modeling (PCA, OPLS), metabolite identification,
and visualisation. Core functions are accelerated in C++ via \pkg{Rcpp},
\pkg{RcppArmadillo}, and \pkg{RcppEigen} for improved computational performance.
}
\section{Features}{

\itemize{
\item Import, preprocessing, and analysis of 1D NMR spectra.
\item \strong{Principal Components Analysis (PCA)} with \emph{back-scaled} loadings
(projected back to the spectral domain and visualized as spectra).
\item \strong{Orthogonal Partial Least Squares (OPLS)} fitted iteratively via the NIPALS algorithm,
with an \emph{automatic stopping criterion} to determine the optimal number of components.
\item Automatic model selection using cross-validated performance (\eqn{R^2}, \eqn{Q^2},
and cross-validated AUC for classification), with safeguards against overfitting.
\item Robust statistical validation for small to large sample sizes:
stratified Monte Carlo cross-validation and k-fold CV.
\item Model diagnostics and validation (DModX, permutation testing).
\item Metabolite identification via STOCSY and STORM.
\item Native C++ acceleration via \pkg{RcppArmadillo} and \pkg{RcppEigen}.
}
}

\section{Vignettes}{

\itemize{
\item Getting Started: \code{vignette("Getting Started")}
}
}

\seealso{
Useful links:
\itemize{
  \item \url{https://tkimhofer.github.io/metabom8/}
  \item Report bugs at \url{https://github.com/tkimhofer/metabom8/issues}
}

}
\author{
\strong{Maintainer}: Torben Kimhofer \email{tkimhofer@gmail.com} (\href{https://orcid.org/0000-0001-7158-9930}{ORCID})

}
