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Changelog

Source: NEWS.md

DeCovarT 2.3.1

  • CRAN resubmission. Tests no longer write under the package tree. The bivariate toy scenario is built in memory by new_bivariate_toy_scenario() in tests/testthat/helper.R; the former fixtures/make-useful-things.R writer and its golden RDS files are gone. CRAN Quarto vignettes do not execute library(DeCovarT) during rebuild (Windows CLI subprocess cannot see R CMD build’s temporary library).

DeCovarT 2.3.0

  • Log-likelihood evaluation. loglik_multivariate() now uses the cached Cholesky factor with backsolve() for the Mahalanobis term, matching mvtnorm::dmvnorm(..., log = TRUE) up to ((2)), rather than a dense ({}{-1}). The inverse remains cached for the analytic score and Hessian.

  • Corrected log-likelihood (breaking numerical change). loglik_multivariate() implemented instead of the Gaussian , doubling the determinant contribution. The objective now matches mvtnorm::dmvnorm(..., log = TRUE) up to , and holds exactly, so the objective and the Wald / Fisher inference are finally consistent. gradient_loglik_unconstrained() and hessian_loglik_unconstrained() halve their determinant terms accordingly; residual terms and expected_fisher_unconstrained() are unchanged. Reported log-likelihood values, AIC and likelihood-ratio statistics all change; point estimates move only slightly. The article and the derivatives vignette were updated in step.

  • Likelihood-ratio and boundary inference. New lrt_decovart(), confint_profile_decovart(), profile_loglik_decovart(), restricted_mle_decovart(), chi_bar_square_pvalue() and bootstrap_decovart(). Testing the absence of a cell type puts the null on a simplex face, where Wilks’ theorem fails and ALR Wald intervals are undefined; the null law is the chi-bar-square mixture of Chernoff (1954) and Self and Liang (1987), with a restricted parametric bootstrap when the binomial weights cannot be justified. Profile intervals are reparametrisation-invariant and stay inside . reference_bootstrap_decovart() resamples the experimental units of a labelled reference: donors within each cell type (default), cells within each cell type, or Dirichlet draws of the composition. Gene-order and cell-type-label shuffles of an averaged signature are not inferential procedures; equivariance_check_decovart() only verifies that permuting signature columns relabels .

  • Boundary and multimodality diagnostics. New boundary_diagnostics() and multistart_decovart(), wired into fit_decovart(n_starts =, boundary_tol =) and stored in fit$diagnostics. The realised log-likelihood is not globally concave (a worked indefinite-Hessian counterexample is in the new vignette), so converged, local_maximum, near_boundary and multimodal are reported as separate claims. A near-boundary estimate is flagged as a caution about Wald linearisation, not as optimiser failure.

  • Numerical stability of additive_logistic(). Now evaluated through the log-sum-exp shift instead of exp(rho) / sum(exp(rho)), which overflowed to NaN for and could make non-factorisable when the MLE approached a simplex face.

  • New vignette vignette("DeCovarT-MLE-properties"): identifiability, existence, failure of uniqueness for one observed sample, population consistency through the Kullback–Leibler divergence and the Fisher information metric, affine (but not logarithmic) equivariance, the four strata of the simplex and their tangent cones, and why replication is what makes the asymptotics meaningful.

DeCovarT 2.2.3

  • Optional heatmap stack. Moved ComplexHeatmap, circlize, and viridis from Imports to Suggests. plot_correlation_Heatmap() guards with requireNamespace() and a clear install message. Removed Additional_repositories (Bioconductor is a standard CRAN dependency source; that field was causing the availability ? ? NOTE).

DeCovarT 2.2.2

  • CRAN resubmission. Quarto Markdown tables in the two CRAN vignettes (no tinytable during vignette rebuild on Windows); absolute pkgdown URLs for articles excluded from the tarball; Rd figure widths in pixels; cran-comments clarifies DESCRIPTION Hunspell false positives.

DeCovarT 2.2.0

  • Model-fit wrapper. Added fit_decovart(), an S3 wrapper in the style of standard R model fits (print, summary, coef, fitted, residuals, vcov, nobs, confint, plot). This makes DeCovarT more versatile and easier for the R statistical community to adopt. deconvolute_ratios() remains the multi-algorithm benchmark tibble. There is no formula / predict() method: the estimator is a variance model, not OLS for bulk expression.

  • fit_decovart() solvers. Marquardt–Levenberg, L-BFGS-B and Newton–Raphson only; ALR maps already land on the simplex (no repair_simplex() on these three).

  • Gene-wise standardise. Affine z-score of bulk, means and covariances (equivariant MLE). Log2 mixing (scaled = TRUE) is rejected (Jensen / CIBERSORT linear space).

  • Wald vcov. Expected Fisher information of the multivariate normal convolution, mapped to the simplex by the ALR delta method.

  • Methods paper on the site. pkgdown embeds article/main.pdf via the embedpdf Quarto extension (vignette DeCovarT methods paper).

DeCovarT 2.0.0

  • Release aligned with the GitHub v2.0.0 tag and the first CRAN submission, focused on numerical stability and optimiser cost in R/03_03_DeCovarT_estimate_ratios_frequentist.R (documented in vignette("generative-model-derivatives"), section Numerical speed-ups and solver safeguards). The CRAN tarball ships the use-cases and softmax/ALR vignettes; remaining articles stay on the pkgdown site.

  • Newton–Raphson evaluation budget. Removed an erroneous eval.max = 1 control passed to stats::nlminb() in deconvolute_ratios_Newton_Raphson(), which capped the entire run at a single objective evaluation and silently returned the equi-balanced start.

  • Cached Cholesky factorisation of \boldsymbol{\Sigma}(\boldsymbol{p}). New internal .sigma_p_factorisation() assembles the mixture covariance once per trial point, shares chol() / chol2inv() across the log-likelihood, gradient and Hessian, and uses a Cholesky-based log-determinant (verified against numDeriv).

  • Analytic gradient for L-BFGS-B. deconvolute_ratios_L_BFGS_B() now passes the unconstrained analytic score instead of finite differences, with finite-penalty guards when box-constrained line searches drive \boldsymbol{\Sigma}(\boldsymbol{p}) near-singular.

  • marqLevAlg Hessian sign under maximisation. When minimize = FALSE, marqLevAlg only negates fn / gr; the analytic Hessian must be negated by hand so the Commenges et al. RDM criterion can fire. Reported upstream as VivianePhilipps/marqLevAlgParallel#3.

  • Documentation. Expanded use-cases and feature-selection vignettes; CRAN-oriented DESCRIPTION (MIT licence, arXiv method reference doi:10.48550/arXiv.2309.09557).

DeCovarT 1.0.0

  • First stabilised release of DeCovarT (semver 1.0.0), marking the end of the exploratory 0.x series. The core ALR-based frequentist deconvolution API, analytic score equations, and simulation tooling are now treated as a stable public surface for downstream use and paper reproduction.

  • Analytic derivatives, numerically verified. The unconstrained and constrained log-likelihood gradients and Hessians (and the additive logistic Jacobian / Hessian) are derived in closed form and unit-tested against numDeriv finite differences. Earlier faulty numerical / finite-difference-only paths that could mislead Marquardt–Levenberg and related optimisers have been replaced by these verified analytic expressions (see vignette("generative-model-derivatives") and tests/testthat/test-03_03_DeCovarT.R).

  • Simulation framework beyond the bivariate toy. Synthetic first- and second-order moments now support arbitrary gene panels (G\gg 2) and multi-type mixtures: AutoGeneS-style mean signatures with a cosine dial, graph-constrained precisions (ER, hub/star, scale-free, SBM, small-world), and bulk convolution via simulate_bulk_mixture(). A hybrid multi-topology reference scenario (G=50, J=3) in scripts/generate_random_markov_network.R and vignette("synthetic-scenarios") stresses feature selection under EE / DE / differential-modality-like blocks (scDD / muscat-inspired taxonomy).

  • Feature-selection metrics (compute_average_overlap(), compute_average_jeffreys(), compute_glmnet_gene_scores()) and a shared check_true_theta() validator complete the end-to-end simulation → pre-screen → NSGA-II refinement loop documented in vignette("feature-selection").

DeCovarT 0.1.0

  • First official release of DeCovarT: bulk transcriptomic deconvolution that accounts for gene-gene covariance in purified reference populations.