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Changelog

Source: NEWS.md

metabodeconplus 0.22.4

  • Added a citation entry: citation("metabodeconplus") now returns Schmidt et al. (2026), Metabolites 16(9):604, doi:10.3390/metabo16090604, and Haeckl et al. (2021) for the original algorithm.

  • The package description, README and Model Fitting article now reference Schmidt et al. (2026).

  • README now presents CRAN as the stable source and GitHub as the development version, and links the Model Fitting and Datasets articles.

  • Documentation fixes: titles and vignettes now say metabodeconplus instead of Metabodecon, and the Contributing article describes how to run the tests, install the package and prepare a release.

  • CI: bumped GitHub Actions versions and allowed manual runs of R-CMD-check.

metabodeconplus 0.22.3

  • snap_to_ref() no longer returns a zero-column feature matrix when it is handed spectra that did not pass through clupa(). It already derived a missing pcial for the reference spectrum but not for the others, so every non-reference peak snapped to NA and si_mat() dropped it – silently, with no error. The same fallback now applies to every spectrum. Results on the normal path are unchanged, since clupa() always sets pcial.

metabodeconplus 0.22.2

  • Runtime improvement: fit_mdm() and benchmark() now skip the up-front $deg grid search when no pipeline stage reads it, i.e. for npmax = 0 (literal deconvolution parameters) and for decon_fun = identity2, where benchmark() previously re-ran the whole grid search once per outer fold and discarded the result. No result changes anywhere; only non-default configurations are affected. decon_fun is not reachable through the exported API (identity2 is internal), so of the two only npmax = 0 can be triggered by a public fit_mdm() / benchmark() call; the default npmax = -1 still needs the grid.

metabodeconplus 0.22.1

  • Improvement: make calc_prarp() clamp both scores at zero, so prarp and prarpx stay in [0, 1]. Practically irrelevant, because the residual is never bigger than the spectrum area for any reasonable deconvolution, but makes the implementation match the theoretical formulation.

metabodeconplus 0.22.0

CRAN release: 2026-08-09

  • CRAN resubmission addressing the review of 0.21.0, which still saw changes of options() and par() without an appropriate reset in R/plot.R and R/util.R. No user-facing API changes.

  • Removed the private multi-figure helpers set_fig() and local_fig(). set_fig() changed par(fig=, new=) and returned a reset function that its two callers registered via on.exit() / withr::defer(), so the reset sat in a different function than the par() call it reverts. That logic now lives in with_fig() and in draw_spectrum(), which change par() and register the restoring on.exit() handler in the same function, before par() is touched. Plot output is unchanged.

  • Removed the unused private helper catft(), which permanently set the metabodeconplus.catft.time option, and dropped the equally unused options(metabodeconplus.aki_cache=) assignment from .onLoad(). The package no longer sets any global option that outlives a function call.

metabodeconplus 0.21.0

  • fit_mdm() and benchmark() now default to model = "ranger" (probability random forest) instead of "lasso". Ranger is the intended default published model; pass model = "lasso" for the L1-penalised logistic-regression backend.
  • ranger moved from Suggests to Imports: it is the default model backend, so it is now a hard dependency and its availability is no longer checked conditionally. speaq moved from Imports to Suggests, since it is only used by the non-default align(use_speaq = TRUE) path.
  • CRAN resubmission addressing the review of 0.20.2. No user-facing API changes beyond the removal of install_mdrb() / check_mdrb_deps().
    • Removed the exported install_mdrb() and check_mdrb_deps() functions: packages must not install other packages (CRAN policy). The optional Rust backend mdrb is now purely user-installed. When deconvolute(use_rust >= 1) is requested but mdrb is missing, check_mdrb() stops with an error that prints the exact install.packages("mdrb", repos = "https://spang-lab.r-universe.dev") command and links to https://github.com/spang-lab/mdrb.
    • Documentation examples no longer use \dontrun{}: runnable examples on the public sim / sim2 datasets are now unwrapped or wrapped in \donttest{}, and no example uses more than two cores.
    • Removed the metabodeconplus::: (triple-colon) references from the harmonize_grid() and fit_mdm() / benchmark() documentation.
    • No longer set options(warn = -1) anywhere (removed together with check_mdrb_deps()).
    • Internal development helpers no longer write to .GlobalEnv or change par() without an immediate on.exit() / withr restore.

metabodeconplus 0.20.2

  • Gave metabodeconplus a distinct Title and Description in DESCRIPTION so they no longer duplicate the CRAN metabodecon package. The title now mentions model fitting, and the description highlights the end-to-end model-fitting workflow (fit_mdm() / benchmark()) and states that metabodeconplus is the backwards-incompatible successor to metabodecon.
  • CI: the slow, network-dependent tests now run on at least one runner per OS. R-CMD-check.yaml promotes the macOS and Windows release jobs from fast to all (RUN_SLOW_TESTS=TRUE), so OS-specific slow tests (e.g. the persistent datadir() test, which is skip_on_os("linux")) keep their coverage. Download failures skip gracefully via skip_if_no_example_datasets(), so the slow jobs do not flake on transient network errors.

metabodeconplus 0.20.1

  • Fixed a flaky Windows R CMD check failure in the glmnet/lasso fit_mdm() and benchmark() smoke tests. glmnet’s compiled code intermittently triggers a Windows access violation (exit code 0xC0000005) when run inside a testthat parallel worker, crashing the test subprocess. The fault is upstream and independent of how fit_lasso() drives glmnet — it reproduces identically with random folds, stratified folds, a manual cross-validation loop, and even the Gaussian family — and it does not occur outside the parallel-worker context. The lasso backend is an optional/secondary path (the default published model, ranger, is unaffected). These lasso smoke tests are therefore skipped on Windows only in automated check environments — CI and CRAN / R CMD check, including win-builder — while still running during local interactive development on Windows and on Linux/macOS everywhere. The ranger tests run on all platforms.

metabodeconplus 0.20.0

  • First release of metabodeconplus, the continuation of the metabodecon package under a new name. It provides an integrated workflow for 1D NMR spectra: deconvolution, alignment, feature-matrix construction and classification models (fit_mdm() / benchmark()), with an optional Rust backend (mdrb).
  • The classic metabodecon (1.6.3) remains available separately, so existing workflows keep working while metabodeconplus evolves. As a fresh 0.x package, metabodeconplus does not yet make backwards-compatibility promises.