smith-group.r-universe.dev

[smith-group] fitnmr 1.1

colin.smith@wesleyan.edu (Colin Smith) — Wed, 13 May 2026 15:17:15 GMT

Tools for fitting and analyzing 1D-4D nuclear magnetic resonance spectra with analytical models of peak shapes and peak groups. The package reads spectra in 'NMRPipe' format, builds constrained parameter structures for chemical shifts, line widths, scalar couplings, volumes, and phases, and performs nonlinear least-squares optimization for iterative peak discovery or simultaneous fits across multiple spectra. It also provides methods for visualization, preprocessing, and kinetic analysis of 1D time-series data, including automated phase optimization, solvent suppression, time-domain correction for frequency shifts and line broadening, modeling spectra as linear combinations of two component spectra, and exponential rate fitting.

[smith-group] sparseLM 0.5

colin.smith@wesleyan.edu (Colin Smith) — Mon, 30 Mar 2026 13:41:29 GMT

Provides an R interface to the 'sparseLM' C library for large-scale nonlinear least squares problems with arbitrarily sparse Jacobians. The underlying solver implements a sparse variant of the Levenberg-Marquardt algorithm for minimizing sum-of-squares objective functions, supports user-supplied analytic Jacobians or finite-difference approximation, and is designed to exploit sparsity for improved memory use and performance. This package exposes the solver in R and uses sparse matrix classes and the 'CHOLMOD' sparse Cholesky factorization routines through the 'Matrix' package interface. Methods from the C library are described in Lourakis (2010) .

[smith-group] deeppicker 0.5

colin.smith@wesleyan.edu (Colin Smith) — Fri, 13 Mar 2026 18:50:54 GMT

Provides an R interface to the DEEP Picker neural-network peak-picking tools for one- and two-dimensional NMR spectra. The package wraps the peak-picking engines, returning peak positions, intensities, line-shape parameters, and confidence scores. It also includes readers for supported spectrum formats, including NMRPipe, Sparky, TopSpin ASCII, JSON, CSV, and ldw files, so spectra can be imported and processed directly.