Fix CRAN readiness: correct DOI, cap RcppParallel threads, add LICENSE/NEWS

- Fix DOI typo: s41467-022-29233-8 → s41467-022-29310-8 (7 locations)
- Add .onLoad() thread cap (2 threads) per CRAN policy
- Add LICENSE.md and NEWS.md; exclude LICENSE.md from tarball
- Add cran-comments.md; update .Rbuildignore
- R CMD check --as-cran: 0E/0W/2N (new submission + time check only)

Author: Tim Tsang

.Rbuildignore

@@ -8,3 +8,5 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^cran-comments\.md$
+^LICENSE\.md$

DESCRIPTION

@@ -14,7 +14,7 @@ Description: A Bayesian framework for inferring influenza infection status from
     probabilities, antibody boosting and waning after infection, and baseline HAI
     titer distributions via MCMC. Supports multi-season analysis and subgroup
     comparisons via a group_by interface. See Tsang et al. (2022)
-    <doi:10.1038/s41467-022-29233-8> for methodological details.
+    <doi:10.1038/s41467-022-29310-8> for methodological details.
 License: GPL (>= 2)
 Encoding: UTF-8
 LazyData: TRUE

LICENSE.md

@@ -0,0 +1,27 @@
+# GNU GENERAL PUBLIC LICENSE
+
+Version 2, June 1991
+
+Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+## Preamble
+
+The licenses for most software are designed to take away your freedom to share
+and change it. By contrast, the GNU General Public License is intended to
+guarantee your freedom to share and change free software — to make sure the
+software is free for all its users. This General Public License applies to most
+of the Free Software Foundation's software and to any other program whose
+authors commit to using it. (Some other Free Software Foundation software is
+covered by the GNU Lesser General Public License instead.) You can apply it to
+your programs, too.
+
+Full license text: <https://www.gnu.org/licenses/gpl-2.0.html>
+
+---
+
+**seroreconstruct** is copyright (C) 2022 Tim Tsang and is distributed under
+the terms of the GNU General Public License, version 2 or later (GPL-2+).

NEWS.md

@@ -0,0 +1,47 @@
+# 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>

R/seroreconstruct-package.R

@@ -8,3 +8,9 @@
 #' @importFrom graphics layout par plot abline axis box lines points legend polygon segments
 #' @importFrom stats quantile density median acf
 NULL
+
+.onLoad <- function(libname, pkgname) {
+  # CRAN policy: packages must not use more than 2 threads during checks.
+  # Users can override via RCPP_PARALLEL_NUM_THREADS environment variable.
+  RcppParallel::setThreadOptions(numThreads = 2L)
+}

cran-comments.md

@@ -0,0 +1,29 @@
+# CRAN submission comments — seroreconstruct 1.1.0
+
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+### Note 1: New submission
+```
+N  checking CRAN incoming feasibility
+   Maintainer: 'Tim Tsang <timkltsang@gmail.com>'
+   New submission
+```
+This is a new submission; the package is not currently on CRAN.
+
+## Thread policy
+
+RcppParallel threads are capped to 2 in `.onLoad()` per CRAN policy.
+Users can override via the `RCPP_PARALLEL_NUM_THREADS` environment variable.
+
+## Reverse dependencies
+
+None — this is a new submission.
+
+## Tested on
+
+- macOS (local): R 4.4.x
+- Ubuntu 22.04 (GitHub Actions, `release`)
+- Ubuntu 22.04 (GitHub Actions, `devel`)
+- Windows Server 2022 (GitHub Actions)

man/seroreconstruct-package.Rd

@@ -25,7 +25,7 @@ over time, and measurement error — estimating individual-level infection
 probabilities from hemagglutination inhibition (HAI) titer data.
 
 The statistical framework is described in
-[Tsang et al. (2022) *Nature Communications* 13:1557](https://doi.org/10.1038/s41467-022-29233-8).
+[Tsang et al. (2022) *Nature Communications* 13:1557](https://doi.org/10.1038/s41467-022-29310-8).
 
 ## Input data
 
@@ -185,4 +185,4 @@ To cite seroreconstruct in publications:
 > Malik Peiris JS, Leung GM, Cowling BJ, Cauchemez S. (2022).
 > Reconstructing antibody dynamics to estimate the risk of influenza virus
 > infection. *Nature Communications* 13:1557.
-> doi: [10.1038/s41467-022-29233-8](https://doi.org/10.1038/s41467-022-29233-8)
+> doi: [10.1038/s41467-022-29310-8](https://doi.org/10.1038/s41467-022-29310-8)

vignettes/introduction.Rmd

@@ -26,7 +26,7 @@ The model accounts for:
 - Heterogeneity in baseline titers and infection risk
 
 The full statistical details are described in
-[Tsang et al. (2022) *Nature Communications* 13:1557](https://doi.org/10.1038/s41467-022-29233-8).
+[Tsang et al. (2022) *Nature Communications* 13:1557](https://doi.org/10.1038/s41467-022-29310-8).
 
 ## Notation
 
@@ -155,7 +155,7 @@ Tsang TK, Perera RAPM, Fang VJ, Wong JY, Shiu EY, So HC, Ip DKM,
 Malik Peiris JS, Leung GM, Cowling BJ, Cauchemez S. (2022).
 Reconstructing antibody dynamics to estimate the risk of influenza virus
 infection. *Nature Communications* 13:1557.
-doi: [10.1038/s41467-022-29233-8](https://doi.org/10.1038/s41467-022-29233-8)
+doi: [10.1038/s41467-022-29310-8](https://doi.org/10.1038/s41467-022-29310-8)
 
 Geyer CJ. (1992). Practical Markov chain Monte Carlo. *Statistical Science*
 7(4):473–483.