metabom8: A High-Performance R Package for Metabolomics Modeling and Analysis

metabom8 (pronounced 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 Rcpp, RcppArmadillo, and RcppEigen for improved computational performance.

Features

• Import, preprocessing, and analysis of 1D NMR spectra.

• Principal Components Analysis (PCA) with back-scaled loadings (projected back to the spectral domain and visualized as spectra).

• Orthogonal Partial Least Squares (OPLS) fitted iteratively via the NIPALS algorithm, with an automatic stopping criterion to determine the optimal number of components.

• Automatic model selection using cross-validated performance (\(R^2\), \(Q^2\), and cross-validated AUC for classification), with safeguards against overfitting.

• Robust statistical validation for small to large sample sizes: stratified Monte Carlo cross-validation and k-fold CV.

• Model diagnostics and validation (DModX, permutation testing).

• Metabolite identification via STOCSY and STORM.

• Native C++ acceleration via RcppArmadillo and RcppEigen.

Vignettes

• Getting Started: vignette("Getting Started")

See also

Useful links:

• https://tkimhofer.github.io/metabom8/

• Report bugs at https://github.com/tkimhofer/metabom8/issues

Author

Maintainer: Torben Kimhofer tkimhofer@gmail.com (ORCID)