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: 2026-11-03 09:17:41 UTC; root
Repository: https://rfeissiv.r-universe.dev
Date/Publication: 2026-03-08 07:03:38 UTC
RemoteUrl: https://github.com/cran/GALAHAD
RemoteRef: HEAD
RemoteSha: d4dae00576659e07f0bf7e76fe7d98c52d190b27