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seroreconstruct 1.1.5

Bug fixes

  • Reduced total check time from >10 min to ~3 min by sharing pre-computed MCMC fixtures across test files and reducing vignette iterations.

  • Added inst/WORDLIST for domain-specific terms (HAI, hemagglutination, titer) flagged by CRAN spell checker.

  • Fixed GPL license badge URL in README that caused a connection timeout on CRAN's Windows pre-test server.

seroreconstruct 1.1.3

Bug fixes

  • Platform-conditional LAPACK linkage via configure/Makevars.in/cleanup scripts, fixing macOS Abort trap from double-linking while retaining Linux dpotrf_ symbol resolution.

  • .onLoad() now respects pre-existing RCPP_PARALLEL_NUM_THREADS before capping to 2.

  • Plot test examples wrapped in pdf(NULL)/dev.off() to prevent Rplots.pdf artifacts.

  • plot_diagnostics() example limited to 2 parameters to avoid graphics device overflow in pkgdown.

seroreconstruct 1.1.2

Bug fixes

  • Added LAPACK/BLAS linkage to src/Makevars for Linux/Debian, fixing undefined symbol: dpotrf_ installation failure on CRAN's Debian (clang-21) pre-test environment.

seroreconstruct 1.1.1

Bug fixes

  • Fixed variable length array (VLA) warnings in C++ code flagged by GCC 14 on Windows (-Wvla). Replaced with std::vector<double>.

  • Removed obsolete CXX_STD = CXX11 from Makevars files and SystemRequirements — the default C++ standard is sufficient.

seroreconstruct 1.1.0

New features

  • sero_reconstruct() gains a group_by argument for subgroup analysis — fit independent MCMCs for age groups, vaccination status, or other strata defined by a one-sided formula (e.g., ~age_group).

  • sero_reconstruct() gains a shared argument for joint models — run a single MCMC that shares measurement error ("error") and/or antibody boosting/waning ("boosting_waning") across groups while estimating group-specific infection risk. Measurement error is always shared when comparing groups of the same virus subtype.

  • sero_reconstruct() gains a subject_ids argument for ID-based individual lookup in plot_trajectory().

  • Multi-season support — add a 0-indexed integer season column to input data; the model estimates season-specific infection risk and HAI protection parameters.

  • S3 classes seroreconstruct_fit, seroreconstruct_joint, and seroreconstruct_multi with print() and summary() methods.

  • New plot functions: plot_trajectory(), plot_boosting(), plot_waning(), plot_infection_prob(), plot_diagnostics().

  • New table functions: table_parameters(), table_infections().

  • simulate_data() — generate synthetic HAI titer datasets for validation and power analysis.

Deprecated

  • output_model_estimate() is deprecated. Use table_parameters() and table_infections() instead.

seroreconstruct 1.0.0

  • Initial release. Core Bayesian MCMC framework for inferring influenza infection status, antibody dynamics, and individual infection risks from longitudinal HAI titer data.

  • Based on Tsang TK et al. (2022) Nat Commun 13:1557. https://doi.org/10.1038/s41467-022-29310-8