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.
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.
src/Makevars for Linux/Debian, fixing
undefined symbol: dpotrf_ installation failure on CRAN's Debian
(clang-21) pre-test environment.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.
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.
output_model_estimate() is deprecated. Use table_parameters() and
table_infections() instead.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