Package: GALAHAD
Type: Package
Title: Geometry-Adaptive Lyapunov-Assured Hybrid Optimizer with
        Softplus Reparameterization and Trust-Region Control
Version: 2.0.0
Authors@R: 
    person("Richard A.", "Feiss",
           email = "feiss026@umn.edu",
           role = c("aut", "cre"),
           comment = c(ORCID = "0009-0008-0409-6042"))
Author: Richard A. Feiss [aut, cre] (ORCID:
    <https://orcid.org/0009-0008-0409-6042>)
Maintainer: Richard A. Feiss <feiss026@umn.edu>
Description: Implements the GALAHAD algorithm (Geometry-Adaptive
    Lyapunov-Assured Hybrid Optimizer), updated in version 2 to replace the
    hard-clamp positivity constraint of v1 with a numerically smooth softplus
    reparameterization, add rho-based trust-region adaptation (actual vs.
    predicted objective reduction), extend convergence detection to include
    both absolute and relative function-stall criteria, and enrich the
    per-iteration history with Armijo backtrack counts and trust-region
    quality ratios. Parameters constrained to be positive (rates,
    concentrations, scale parameters) are handled in a transformed z-space
    via the softplus map so that gradients remain well-defined at the
    constraint boundary. A two-partition API (positive / euclidean) replaces
    the three-way T/P/E partition of v1; the legacy form is still accepted
    for backwards compatibility. Designed for biological modeling problems
    (germination, dose-response, prion RT-QuIC, survival) where rates,
    concentrations, and unconstrained coefficients coexist. Developed at
    the Minnesota Center for Prion Research and Outreach (MNPRO), University
    of Minnesota. Based on Conn et al. (2000)
    <doi:10.1137/1.9780898719857>, Barzilai and Borwein (1988)
    <doi:10.1093/imanum/8.1.141>, Xu and An (2024)
    <doi:10.48550/arXiv.2409.14383>, Polyak (1969)
    <doi:10.1016/0041-5553(69)90035-4>, Nocedal and Wright (2006,
    ISBN:978-0-387-30303-1), and Dugas et al. (2009)
    <https://www.jmlr.org/papers/v10/dugas09a.html>.
URL: https://github.com/RFeissIV/GALAHAD
BugReports: https://github.com/RFeissIV/GALAHAD/issues
Note: Development followed an iterative human-machine collaboration
        where all algorithmic design, statistical methodologies, and
        biological validation logic were conceptualized, tested, and
        iteratively refined by Richard A. Feiss through repeated cycles
        of running experimental data, evaluating analytical outputs,
        and selecting among candidate algorithms and approaches. AI
        systems ('Anthropic Claude' and 'OpenAI GPT') served as coding
        assistants and analytical sounding boards under continuous
        human direction. The selection of statistical methods,
        evaluation of biological plausibility, and all final
        methodology decisions were made by the human author. AI systems
        did not independently originate algorithms, statistical
        approaches, or scientific methodologies.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.2.0)
Imports: stats, utils
Suggests: testthat (>= 3.0.0)
RoxygenNote: 7.3.3
Config/testthat/edition: 3
NeedsCompilation: no
BuildResaveData: true
Packaged: 2026-03-06 20:30:06 UTC; feiss026
Repository: CRAN
Date/Publication: 2026-03-08 06:11:20 UTC
Built: R 4.6.0; ; 2026-04-26 18:40:56 UTC; unix
