High-Performance Open-Source Archive
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
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