serocalculator (development version)

Bug fixes

  • est_seroincidence()’s cluster_var argument can now be pointed at the subject id (e.g. cluster_var = ids_varname(pop_data)) to get a cluster-robust standard error for a multi-biomarker fit that accounts for within-person correlation across biomarkers. log_likelihood() combines biomarkers by summing their marginal log-likelihoods, which understates the true variance when biomarker readings from the same person are correlated, as expected when they share an infection history — see #637. A verbose fit with more than one antigen_isos and no cluster_var now says so, and names the id column to pass. The default behavior (no cluster_var) is unchanged, and its standard error is unaffected. (#645)
  • Restored participant linkage across biomarker rows in the SEES cross-sectional data and bundled examples. Public IDs are newly generated pseudonyms; the restricted source identifier is never written to package artifacts. as_pop_data() and set_id_var() now clarify that their ID column must identify people rather than individual observations. (#650)

New features

  • Added sim_pop_data_multi_cached() and est_seroincidence_by_cached(), caching wrappers around the two most computationally expensive functions in the package. The first call computes and saves the result; later calls with the same arguments load it instead of recomputing. The cache is keyed on the arguments, so changing any of them recomputes automatically. Pass cache_rerun = TRUE to force recomputation. Cache-control arguments carry a cache_ prefix so the wrapped functions’ own verbose argument remains reachable. (#631)
  • Added refit_strata(), which re-fits a chosen subset of strata with log-likelihood graphs attached. It is the companion to caching a large fit with build_graph = FALSE: graphs are attached per stratum, so they make a cached fit far larger on disk, and the usual pattern is to cache without them and re-fit only the strata you want to plot. Strata are selected by the columns that define them rather than by index, because count_strata() names strata positionally and a subset renumbers them. (#632)
  • Added interactive Shiny app curve_app() for visualizing antigen-antibody kinetics models with real-time parameter sliders (#392).
  • Added antibody_decay_curve() and pathogen_decay_curve() functions for simulating antibody and pathogen decay over time (#392).
  • Added plot_decay_curve() for plotting decay functions using ggplot2 (#392).
  • Added helper functions t1f() (time to end of active infection) and y1f() (peak antibody concentration) (#392).
  • autoplot.sim_results() gains x_var, group_var, and color_var arguments, letting users choose which columns map to the x-axis, group, and color aesthetics instead of the previous hardcoded sample_size / lambda.sim mapping.
  • graph.curve.params() now uses the 5-parameter ab_5p() antibody response model and supports units-aware curve parameters. (#393)
  • Added ab_5p(), a 5-parameter antibody response model that supports {units}-aware inputs (e.g. t = units::as_units(50, "days")), building on the existing bt() active-phase helper. CI now installs the system udunits2 library on macOS and Windows so the new units dependency can compile there. (#393)
  • Added sim_pop_data_2(), a sim_pop_data() alternative built on ab_5p() that simulates each simulated individual’s age (sim_age()) and time since their last seroconversion (sim_time_since_last_sc()) directly, rather than simulating an infection history. Both new helper functions, and sim_pop_data_2() itself, accept units-aware inputs.
  • sim_pop_data_multi() gained a sim_function parameter (default sim_pop_data) so callers can select sim_pop_data_2() instead. (#393)

Documentation

  • Split the methodology article’s combined “Likelihood and log-likelihood” definition into two separate, independently cross-referenceable definitions (#def-likelihood, #def-log-likelihood) — previously only the likelihood half had its own citable id.

  • Formalized the “Cluster-robust standard errors” section of the methodology article: the sandwich estimator now cites Huber (1967), White (1980), and the clustered-data extension by Liang and Zeger (1986), and the Hessian, score function, and other definitions and results in that chapter are now stated as numbered, cross-referenced Quarto theorem/definition divs instead of informal prose.

  • The methodology, scrub typhus, and antibody-response-model articles no longer fetch their example data from OSF at render time — the docs build was failing whenever OSF was unavailable, on PRs that never touched the affected vignettes. n6cp3, hqy4v, u5gxh, and h5js4 are now vendored under vignettes/precomputed/osf/; the two chunks that only needed rtw5k filtered to iter < 50 now filter the already-bundled typhoid_curves_nostrat_100 instead, since the two are identical once filtered, so no separate copy of rtw5k needed vendoring. (#648)

  • Removed maintainer-facing implementation notes (OSF/vendoring rationale, an internal variable-naming decision, why est_seroincidence_by_cached() is called with build_graph = FALSE) from the R comments the methodology article renders on the website, replacing them with reader-facing comments. The notes worth keeping for future editors but with no reader-facing equivalent moved into HTML comments, invisible on the published page; a couple of purely build-time asides (e.g. “no network access needed”) were dropped outright as no longer worth keeping.

  • Listed sim_pop_data_multi_cached(), est_seroincidence_by_cached(), and refit_strata() in the documentation site’s reference index. All three were exported and had help pages, but no section of altdoc/reference.yml claimed them, so they were unreachable from the reference index and the sidebar and fell into the trailing “Other” group. Surfaced by altdoc::render_docs(), which warns about an unclaimed non-internal topic; no CI check covers this. (#632)

  • Merged the “Simulation studies” article (vignettes/articles/simulate_xsectionalData.qmd) into the methodology article, which now demonstrates live everything it describes. The methodology article previously showed serocalculator code in non-executing chunks and closed with a static screenshot of the simulation article’s recovery study, while the simulation article ran that code without deriving the theory behind it. The estimation walkthrough now runs on simulated data where the true rate is known, and the validation section runs the full multi-cluster recovery study, the nlm() convergence checks, analyze_sims(), and the renew_params bias caveat. The retired article’s URL redirects to the merged one. (#632)

  • The methodology article’s simulations are cached to vignettes/precomputed/ via the new *_cached() wrappers, so a docs build reuses them instead of recomputing once per output format. Its simulation sections now use the bundled typhoid_curves_nostrat_100 rather than downloading the same curve parameters from OSF; the two are identical once filtered.

  • The methodology article’s reveal.js slides now show code, folded away by default, instead of hiding it. The Word output hides code by default, except in the demonstration chunks that are never evaluated, which mark themselves echo: true so those sections do not render empty.

  • Ported the full Quarto extension set from Morrison-Lab/rpt into altdoc/_extensions/, registered project-wide in altdoc/quarto_website.yml’s new filters: list: d-morrison/div-anchors and d-morrison/equation-anchors add hover permalinks to theorem/definition divs and numbered equations; sun123zxy/callouty-theorem (+ coatless-quarto/custom-callout) render the methodology vignette’s existing #def-/#exm- divs as colored callout boxes instead of plain numbered text; d-morrison/revealjs-html-links adds a link back to the standalone HTML page on the methodology vignette’s RevealJS slides. The slidebreak extension (already in use) moved from vignettes/_extensions/ to altdoc/_extensions/ alongside the rest, so it too is now a project-level filter instead of a per-document one. (#585, #586, #587, #588, #589)

  • Took the sidebar fold control from altdoc instead of keeping a copy here. altdoc/sidebar-fold.html and the matching block in altdoc/styles.css are replaced by include-in-header: $ALTDOC_SIDEBAR_FOLD, which altdoc stages at render time with script and style together. The same pair had been copied into ucdavis/bcs, and the two copies had already drifted – this repo changed its copy to start folded and nothing carried that across. The sidebar still starts folded, now via sidebar_fold: collapsed in altdoc/reference.yml, so what used to be a source-level divergence is a one-line setting.

  • Declared the reference manual’s grouping once, in a new altdoc/reference.yml (#610). It used to live in two hand-maintained places that nothing kept in step: the altdoc/reference.qmd index page and the Reference block of altdoc/quarto_website.yml. Adding a topic to one and missing the other rendered cleanly and raised no warning, which is how it went unnoticed on #392. altdoc now builds both surfaces from the single file, so the two cannot disagree, and warns about any exported topic no section claims rather than leaving it off the site in silence. The published grouping is unchanged: the same nine sections, the same 42 topics, in the same order.

  • Moved the altdoc dependency off the recursive-qmd-search branch and onto the default branch, which is what supplies the grouped sidebar above. That branch has no commits the default branch does not already contain, so it was holding the docs build behind for nothing. The branch was named in three places – Remotes, Config/Needs/website, and the r-packages input of the docs workflow – and changing one of them alone makes the build fail to resolve rather than fall back, since pak reads the two as conflicting requirements for the same package.

  • Started showing each topic’s name alongside its title in the sidebar. Titles alone left as_pop_data and load_pop_data as adjacent entries reading identically, and the same for as_noise_params and load_noise_params, with nothing to tell a reader which was which.

  • Stopped .gitignore from hiding new files added under altdoc/. A bare altdoc entry ignored the whole source directory; the files already in it stayed tracked only because they predate the rule, so the omission was invisible until a new one was added and silently skipped by git add. altdoc/.gitignore already covers the real build artifacts there (_site/, .quarto/, pkgdown.yml, freeze.rds), and _quarto is still ignored separately, so the entry protected nothing.

  • Added a control that folds the documentation website’s sidebar away, giving the content the width it held (#622). Quarto’s collapse-level folds sections within the sidebar; it has no control for the sidebar itself on a website, so the sidebar held a fixed grid column at every viewport wide enough to show it. The new navbar button hides it and moves the content’s grid start line into the vacated columns, which at a 1400px viewport widens the content from 630px to 922px. The state is kept in localStorage, so it survives navigation between pages. The script that restores it is included in the page header rather than after the body, so a folded sidebar never flashes into view. Below Quarto’s 992px breakpoint the button is hidden: the sidebar is already a drawer laid over the content there, so it holds no width to reclaim.

  • The documentation website’s sidebar now starts folded. Readers arrive on a page to read it, and the navbar already carries the same destinations, so the wider content column is the better default; unfolding the sidebar is remembered, so the choice is still made once per reader rather than once per page.

  • Fixed two dead external links. The methodology article credited the Salmonella Typhi photo to a Wikimedia Commons page that was deleted on 2026-03-11; the deletion discussion confirms the image is CDC/PHIL public-domain work (PHIL ID 2115), so the credit now cites PHIL directly instead of the dead page. The Ubuntu R install snippet in .github/copilot-instructions.md fetched pubkey.gpg, which CRAN no longer serves (404); it now uses marutter_pubkey.asc.

  • Figures on the documentation website now open an enlarged lightbox view when selected. Enabled site-wide (lightbox: true) across every format, including the revealjs slides, and covering both cross-referenced figures and plain images (#584).

  • Restored the R code in the documentation website’s vignettes and articles. vignettes/_metadata.yml set echo: false for the html and docx formats, which applied to every file under vignettes/, so the published tutorials rendered as prose and figures with no code at all, and the methodology article’s “Estimating seroincidence” section — whose only content is a non-evaluated code chunk — rendered as an empty heading.

  • Reviewed and revised the methodology article: corrected the standard-error description (the inverse negative Hessian is the variance, not the standard error) and the “truncated by age” characterization of the latent infection-time distribution, added narrative to the previously code-only “Estimating seroincidence” and “Multiple biomarkers” sections, moved “In-progress work” out of the “Validation” section into its own section, promoted “References” to a top-level section, and restored the captions and image credits on the two typhoid figures (adjacent images with no blank line between them are parsed as one paragraph, which drops their captions).

  • Fixed dead documentation links that still used the old pkgdown site layout. The site root is now a redirect page, so /articles/…, /reference/index.html, /news/index.html, and /CONTRIBUTING.html no longer resolve; links from within the site are now relative so they stay on the reader’s docs version, and the links in the README point at paths that exist. Also corrected the description in the README of which URL serves which docs version, and fixed the link to the contributing guide in the pull request template.

  • Fixed a dead link in the README: the in-development documentation pointed at /main/, which has served nothing since #504 moved development docs to /dev/. Also removed a duplicated “the” in the same sentence. (#604)

  • The documentation site now deploys multiple versions side by side, following rpt’s pattern: pushes to main deploy development docs to /dev/, published releases deploy stable docs to /latest-tag/ (plus an archived /vX.Y.Z/ copy), and the site root redirects to whichever was deployed most recently. A “Versions” navbar dropdown links between them. (#504)

  • Updated the documentation site configuration to promote “Get started”, “Reference”, and “News” in the top navigation, and added a grouped reference.qmd index plus grouped sidebar reference sections that exclude internal-only topics.

  • The documentation site’s reference index page is now titled “Package index” rather than “Reference”, matching the old pkgdown site and distinguishing the page from the navigation entry that links to it. (#594)

  • Added a “Citation” entry to the documentation site’s sidebar. The citation page was previously reachable only from the navbar “More” dropdown, unlike rpt and the default sidebar altdoc ships, which both list it. (#594)

  • Links to the documentation site’s old /main/ paths now resolve again. Before the altdoc migration the development docs were published under the branch name, so they lived at /main/; they now live at /dev/, which left every /main/... link dead. The site now serves a root 404.html that redirects any request under /main/ to the same path under /dev/, deep links included. Redirection requires JavaScript; without it the page renders as a plain not-found notice linking to the documentation home page. (#599)

  • Updated the documentation site’s dark-mode styling to match rpt by adding the same inline-code color override used there, improving contrast on the home page and article text.

  • Added introductory lecture slides to the methodology vignette (“Estimating Incidence Rates from Cross-Sectional Serosurveys”).

  • The methodology vignette now loads its slidebreak shortcode explicitly so the shortcode no longer leaks into HTML output, and rendered vignettes now suppress package startup messages.

  • Fixed the date in the vignettes’ title blocks, which rendered as “Invalid Date” (most visibly on the methodology slides’ title slide). vignettes/_metadata.yml set the date with an inline R expression, but Quarto merges that file into the document metadata without a knitr pass, so the expression was never evaluated; the date now uses Quarto’s own today keyword. (#597)

  • Restored the methodology vignette’s docx download link, which had been dropped on the (mistaken) assumption that it needed its own docx: format block; it renders fine via the docx: default already declared in vignettes/_metadata.yml.

  • Completed the measurement-noise model in the methodology vignette (multiplicative relative error), added a “Combined biological and measurement noise” section, and added a “Noise and never-infected subjects” section explaining that additive biological noise spreads a never-infected subject’s measured response over a positive range while multiplicative measurement noise leaves a true zero at zero. (#561)

  • Corrected the documentation of the eps measurement-noise parameter (in example_noise_params_pk/example_noise_params_sees and the vignettes): eps is the bound on the relative measurement error (Unif(-eps, eps)), not a coefficient of variation. A measured CV corresponds to eps = sqrt(3) * CV. (#563)

  • Added the never-infected density under combined biological and measurement noise to the methodology vignette: the piecewise closed form for y_obs = eps_b * (1 + xi), matching Teunis and van Eijkeren (2020) Equation 19 and verified to integrate to the never-infected probability. (#567)

  • Made the never-infected term explicit in the “per-person likelihood” slide of the methodology vignette: the observed-data likelihood integral is now shown split into its continuous (ever-infected) and discrete (T = NA, never-infected) parts, with p(Y=y | T=NA) defined as a point mass at zero (before noise). (#567)

  • Explained, in the “Biological noise” section of the methodology vignette, why the biological-noise width nu is estimated as the 95th percentile of negative controls: Teunis and van Eijkeren (2020) show that a uniform noise model only needs to match the true noise distribution’s width, not its exact shape, and note that this width is difficult to verify against a mixed (ongoing-seroresponse) population – motivating estimation from a clean negative-control panel instead. Also noted that the specific choice of the 95th percentile (rather than, e.g., the 99th or the sample maximum) is an adopted convention, not a result derived or optimized in the paper. (#567)

  • Added the conditional variance Var(y_obs | y_true) for the combined biological- and measurement-noise model to the methodology vignette, derived from the independent-product-variance identity and checked against both single-source special cases already in the vignette. (#571)

  • Added Var(y_obs | T=t), marginalizing over between-person heterogeneity in y_true, to the methodology vignette: derived via the law of total variance from the Var(y_obs | y_true) formula above, with the between-person heterogeneity term Var(y_true | T=t) introduced symbolically (it has no closed form in this framework, since serodynamics represents curve-parameter heterogeneity as an empirical posterior sample rather than a stated parametric distribution). Clarified that the longitudinal model’s residual variance is constant on the log scale conditional on individual random effects, while random waning rates can induce time-varying marginal population variance that serocalculator carries forward by averaging over kinetic-parameter draws. (#571)

  • Moved f_dev0()’s @examples block to a separate example file (inst/examples/exm-f_dev.R), following the convention already used by other functions in this package. (#393)

Internal

  • Added a regression test locking in that multi-biomarker log_likelihood() equals the sum of the per-biomarker values. This is the composite (independence) likelihood behavior described in #637: the code sums per-biomarker marginal log-likelihoods rather than integrating a shared latent infection time, and this identity should not change silently if that ever does. (#637)
  • Regenerated NAMESPACE and DESCRIPTION with roxygen2 8.1.0, which groups each package’s importFrom() symbols into a single multi-line directive instead of one directive per symbol. The change is purely one of formatting: the exports, the S3 method registrations, the compiled-library declaration, and all 75 imports are unchanged. docs-check regenerates the documentation and fails when a tracked file differs afterward, so every run of it since roxygen2 8.1.0 was published on 2026-08-04 had failed. Green docs-check runs on other open pull requests are stale rather than contradictory: each of them predates that release. (#636)
  • Disabled the @claude agent bot. .github/workflows/claude.yml’s reactive triggers are commented out and its job carries if: false, so no comment, issue, or review event invokes the agent, and neither does a manual dispatch (the reusable workflow runs unattended on workflow_dispatch by design). Reviews are the only Claude capability left, and they run on request only: automatic review on pull-request activity is off, and a review starts when a collaborator comments /review on a pull request. That dispatch now pins the review run to the pull request’s head branch, so its check-run lands on the right commit.
  • Fixed two dead provenance links in workflow comments. check-readme.yaml cited a file that was deleted from IndrajeetPatil/statsExpressions’s default branch when its CI moved to reusable workflows; the citation is now pinned to a commit where the file exists. test-coverage.yaml cited a GitHub Actions run URL, which expires after roughly 90 days; it now cites the upstream workflow file.
  • Removed .github/CONTRIBUTING.Rmd; .github/CONTRIBUTING.md is now the hand-maintained source. The .Rmd executed no code (its only chunk was eval = FALSE), so it rendered to markdown identical to a hand-written file while adding a source/generated pair with no CI check to keep the two in sync. (#613)
  • Documentation website now renders HTML (primary), docx (download link on every page), and revealjs (slides for methodology.qmd) formats. Fixed the HTML/revealjs output-filename collision by specifying output-file: methodology-slides.html for revealjs in methodology.qmd’s frontmatter; docx goes in _metadata.yml globally since .docx has no collision risk. (#503)
  • Added Codex repository guidance and R-package workflow skills. (#574)
  • news.yaml now calls the central d-morrison/gha check-news.yml@v2 reusable workflow (bumped from the initial @v1 pin, which predated gha’s fix for this repo’s no-changelog label convention) instead of invoking UCD-SERG/changelog-check-action@v2 directly. (#537, #593)
  • claude.yml and claude-code-review.yml now call the central d-morrison/gha claude.yml@v2 and claude-code-review.yml@v2 reusable workflows instead of carrying their own copy of the agent/review machinery. (#549)
  • docs.yaml now calls the central d-morrison/gha altdoc-multiversion-docs.yml@v2 reusable workflow instead of carrying its own ~360-line copy of the build/deploy logic, and the local .github/scripts/generate_version_dropdown.py and generate_multiversion_landing_page.py copies are deleted in favor of the composite actions in that repo. Fixes made centrally now reach this package instead of stopping at rpt. Rewrote .github/MULTI_VERSION_DOCS.md, which still described the pkgdown setup replaced during the altdoc migration. (#595)
  • The methodology vignette’s LaTeX macros now come from the shared d-morrison/macros git submodule (included via {{< include ../macros/macros.qmd >}}) instead of a local vignettes/articles/_macros.qmd. The deck adopts the shared macro vocabulary (e.g. \dens for the density function in place of the local \pdf). (#534)
  • claude-code-review.yml now sets allowed_bots: github-actions[bot] so the review still runs (and posts feedback) when claude.yml re-dispatches it on an @claude review comment; previously the bot-initiated dispatch aborted with “Workflow initiated by non-human actor”.
  • claude.yml now grants the @claude agent the file tools (Read/Glob/Grep/Edit/MultiEdit/Write) in --allowedTools; previously the agent could run checks/git/gh but not edit files, so it fell back to posting diffs for manual application.
  • Added the iterate Claude Code skill (.claude/skills/iterate/) for driving a PR to a clean review verdict.
  • Ported the @claude agent and PR-review GitHub Actions workflows (plus Claude/Copilot config: CLAUDE.md, .claude/ settings and slash commands, and path-scoped .github/instructions/) from the UCD-SERG qwt template, adapted to this package. (#523)
  • Claude PR review workflow now skips (rather than hard-failing) when triggered by a bot (e.g. claude[bot] pushing a commit). (#519)
  • Added the lint-changed-lines CI workflow (calling the reusable d-morrison/gha lint-changed-lines.yml@v2 workflow), which flags lint issues only on the lines a PR actually adds or modifies (rather than whole changed files, as lint-changed-files does). This lets lint rules be adopted or tightened incrementally as code is touched, instead of forcing a repo-wide reformat. Intended to replace lint-changed-files as the lint gate once branch protection is updated to require it. (#558)
  • Removed docs.yaml’s job-level concurrency: group, which resolved to the same string as the workflow-level group on every non-pull_request event and so deadlocked the docs job: the run already held that group, so the job could never acquire it and was failed instantly with no logs. This blocked every versioned documentation deploy (/dev/, /latest-tag/, /vX.Y.Z/). The workflow-level group already serializes runs by PR number or ref. (#590)

Bug fixes

  • sim_pop_data() and sim_pop_data_multi() now produce identical results across operating systems. Simulated inter-infection times are now rounded to whole days, so the number of random draws consumed no longer depends on platform-specific floating-point results of log() (which previously shifted the random-number stream out of sync and made simulated values, and their snapshots, differ between macOS, Windows, and Linux). Simulated values change slightly as a result of this fix. (#447)
  • Cluster-robust standard errors now treat multiple cluster_var columns as multi-way clustering instead of collapsing them to a single interaction. One-way subset terms now use the CR1 small-sample correction by default, the floor to model-based variance is optional, and debug output now exposes the multi-way variance decomposition used in the final standard error. A negative multi-way variance estimate is now floored at 0 (with a warning) instead of producing NaN standard errors, and an unavailable subset variance (for example from a degenerate Hessian) now warns and yields a missing standard error, instead of a silent NaN. With floor_to_standard = TRUE it falls back to the model-based variance instead, unless that variance is itself unusable (e.g. from the same degenerate Hessian), in which case it also yields a missing standard error. (#543)
  • Corrected default axis labels in strat_ests_barplot() (xlab) and strat_ests_scatterplot() (ylab) to say “seroincidence” rather than “seroconversion”/“incidence”.
  • load_noise_params() and load_sr_params() now fail gracefully with informative messages when internet resources are unavailable, complying with CRAN policy (#505)
  • Added Version Crosswalk article to pkgdown website to help users migrate code from v1.3.0 to v1.4.0
    • Provides clear tables comparing old and new function names
    • Includes code examples showing how to update existing code
    • Accessible as a prominent tab in the website navigation
  • autoplot.seroincidence() now raises its “graphs cannot be extracted” error via cli::cli_abort() rather than stop(), so the message is formatted as a cross bullet naming the problem and an info bullet naming the build_graph = TRUE argument that was missing (#392).
  • antibody_decay_curve(), pathogen_decay_curve(), t1f(), and y1f() now validate their parameters (non-negative values, mu_y != mu_b) and raise an informative cli::cli_abort() error instead of silently returning NaN or dividing by zero (#392).
  • plot_decay_curve() now respects its xmax argument instead of always plotting to x = 100 (#392).

Compatibility

  • Replaced deprecated dplyr::is.grouped_df() usage with dplyr::is_grouped_df() in df_to_array() for compatibility with newer dplyr releases.

New features (cluster-robust SE)

  • Added cluster_var and stratum_var parameters to est_seroincidence() and est_seroincidence_by() to support cluster-robust standard error estimation. When cluster_var is specified, summary.seroincidence() automatically computes cluster-robust (sandwich) variance estimates to account for within-cluster correlation in clustered sampling designs such as household or school-based surveys.
  • cluster_var parameter now accepts multiple variables (e.g., c("school", "classroom")) for multi-level clustered sampling designs. Cluster-robust standard errors will account for all specified clustering levels.

Bug fixes (cluster-robust SE)

  • Fixed column naming issue in summary.seroincidence() where cluster-robust standard errors caused [] notation in column names (SE[,1] instead of SE).
  • Added se_type column to summary.seroincidence() output to clearly indicate whether “standard” or “cluster-robust” standard errors are being used.
  • Fixed est_seroincidence_by() to properly pass cluster and stratum variables through to stratified analyses. Previously, these variables were dropped during data stratification, causing errors when trying to use clustering with est_seroincidence_by().

Code organization

  • Refactored clustering-related code following package organization policies:
    • Moved .compute_cluster_robust_var() to R/compute_cluster_robust_var.R
    • Each function now in its own file for better maintainability and git history
  • Updated copilot-instructions.md with code organization policies

Dependencies

  • Replaced ggpubr with patchwork for arranging multi-panel plots, removing the indirect ggrepel transitive dependency.

serocalculator 1.4.0

New features

  • Added support for cluster-robust standard errors in est_seroincidence() through new cluster_var and stratum_var parameters. When cluster_var is specified, summary.seroincidence() automatically computes cluster-robust (sandwich) variance estimates to account for within-cluster correlation in clustered sampling designs such as household or school-based surveys.

  • Added compare_seroincidence() function for statistical comparison of seroincidence rates

    • Performs two-sample z-tests to compare seroincidence estimates
    • Returns htest format when comparing two single estimates
    • Returns formatted table with all pairwise comparisons for stratified estimates
    • Added examples to tutorial vignette and comprehensive unit tests

  • Implemented multi-version pkgdown documentation with version dropdown menu

    • Users can now switch between main, latest-tag, and versioned releases
    • Default landing page shows latest-tag (most recent release)
    • Based on insightsengineering/r-pkgdown-multiversion setup

  • Added chain_color option to graph.curve.params() to control MCMC line color (#455)

  • Made graph.curve.params() the default sub-method for autoplot.curve_params() (#450)

  • Added log_x and log_y options to graph.curve.params() sub-method for autoplot.curve_params() (#453)

  • Extended sim_pop_data_multi() to loop over multiple sample sizes (#444)

  • Added new functions analyze_sims() and autoplot.sim_results() (#444)

  • Rename estimate_scr() to est_seroincidence_by() (#439)

  • Rename estimate_scr() to est_seroincidence() (#432)

  • Rename argument curve_params to sr_params for estimation functions (#424)

  • added documentation for count_strata() (#431)

  • Rename as_curve_params() to as_sr_params() (#421)

  • Rename load_curve_params() to load_sr_params() (#421)

  • added default for xvar in "scatter" option for autoplot.seroincidence.by() (#417)

  • Extended autoplot.summary.seroincidence.by() to include types for either scatter or bar plots of stratified results (#397)

  • added option to add lines using group_var input to autoplot.summary.seroincidence.by() (#410)

  • autoplot.pop_data(type = "age-scatter") now shows legend at bottom (#407)

  • autoplot.pop_data(type = "age-scatter") now facets by antigen isotype (#406)

  • Rename est.incidence.by() to estimate_scr_by() (#389)

  • Rename est.incidence() to estimate_scr() (#389)

  • Improved warning messages for get_biomarker_names_var()

  • Added get_*() extractor functions to API (#380)

  • Added optional CI error bars to autoplot.summary.seroincidence.by() (#372)

  • Improved y-limit calculation in graph.curve.params() (#368)

  • Added option for graph.curve.params() to show all curves (#368)

  • Added color-coding for graph.curve.params() (#383)

  • Added quantiles parameter to graph.curve.params() and corresponding test in test-graph.curve.params.R (#434)

  • Removed warn.missing.strata() from API (#366)

  • Added more details about contributing PRs in Contributing.md (#280)

  • Added warnings for missing biomarker data (#168):

    • completely missing antigen-isotype in a stratum
    • uneven antigen-isotype counts in a stratum (likely from incomplete data)

  • Split dev and release websites into:

    • release: https://ucd-serg.github.io/serocalculator/
    • dev: https://ucd-serg.github.io/serocalculator/dev/

  • Fixed citations in methodology.qmd article (#360)

  • Added outline to pkgdown website (#353)

  • Added verbose option for summary.seroincidence() and summary.seroincidence.by() (#348)

  • Extended simulate_xsectionalData.Rmd article to explore renew_params = TRUE vs renew_params = FALSE (#348)

  • Renamed variables for consistency (#281, #373):

    • sim.cs() -> sim_pop_data()
    • sim.cs.multi() -> sim_pop_data_multi()

Bug fixes

  • Fixed CRAN errors (#464)
  • Fixed stratification issue in enteric fever vignette (#418)
  • Fixed issue in graph.curve.params() where MCMC samples with the same iteration number from different MCMC chains would get merged by ggplot2::aes(group = iter) (#382)

Internal changes

  • switched expect_snapshot_data() to an internal function due to CRAN errors (#464)

  • generalized ab1()

  • added codecov/test-results-action to test-coverage.yaml workflow

  • added test for censored data in f_dev() (#399)

  • added test for autoplot.curve_params()

  • added test for graph.curve.params() (#368)

  • reverted Readme source file from qmd to Rmd.

  • switched pkgdown GHA from any::pkgdown to r-lib/pkgdown (i.e., dev version) (#359)

  • added test for summary.seroincidence.by() (#352)

  • Started checking for use of base pipe instead of magrittr pipe by linter (#347)

  • Removed ldpar() from API (#345)

  • Added test for sim.cs() (#344)

  • Added test for internal function ab() (#342)

  • Reverted name change ldpar()-> row_longitudinal_parameter() (#343)

serocalculator 1.3.0

New features

  • Removed function ‘get_additional_data()’ (#332)

  • Updated documentation examples to include csv files (#328)

  • Added csv files for use in documentation examples (#329)

  • Added serocalculator_example() function to help locate example data files (#329)

  • Fixed a bug in computing the antibody response curve when \(r=1\) (#323)

  • Added example datasets with documentation for examples and testing (#314)

  • Improved error messaging for autoplot.pop_data() (#234).

  • Clarified package installation instructions in scrub typhus vignette (#234).

  • Add as_noise_params (#228)

  • Updated simulate_xsectionalData.Rmd (linting, removing deprecated functions) (#289)

  • Added default value for antigen_isos argument in log_likelihood() (#286)

  • Updated enteric fever example article with upgraded code and visualizations (#290)

  • Added Methodology vignette (#284, #302, #303)

  • Added template for reporting Issues (from usethis::use_tidy_issue_template()) (#270)

  • Added template for pull requests (from https://github.com/bcgov/ssdtools) (#265)

Internal changes

  • Updated documentation to align with previous CRAN feedback (#328)

  • Updated tests to use internal testing datasets instead of external links (#328)

  • Updated test-coverage.yml GHA action to current r-lib standard (#330)

  • Change default pipe setting (#312)

  • Add test for missing strata in est.incidence.by (#227)

  • Added snapshot_value test for est.incidence() (#315)

  • Sped up lint-changed-files GitHub Action (#317)

  • Added online preview builds for PRs that change the pkgdown website (#309)

  • Added test-autoplot.pop_data test (#234)

  • initialized lintr with lintr::use_lint() (#278)

  • created unit test for df_to_array() (#276)

  • fixed dplyr::select() deprecation warning in df_to_array() (#276)

  • Added devtag to package (using devtag::use_devtag()) (#292)

  • Added @dev tag to ?df_to_array() (#292)

  • Generalized get_() and set_() methods to be general-purpose (no S3 class-specific methods needed yet) (#274).

  • Updated GitHub Action files and reformatted DESCRIPTION (#268)

  • Added .gitattributes file (https://git-scm.com/docs/gitattributes) copied from https://github.com/tidyverse/ggplot2

  • Added QR code to README.qmd

  • Added additional automated checks through GitHub actions, including:

serocalculator 1.2.0

  • Added test-summary.pop_data test

  • Modified test-est.incidence test

  • Added stratification to summary.pop_data

  • Added verbose option for check_pop_data(), changing default behavior to avoid printing an OK message.

serocalculator 1.1.0

  • Renamed llik() to log_likelihood()

  • Renamed fdev() to f_dev()

  • Renamed df.to.array() to df_to_array()

  • Renamed getAdditionalData() to get_additional_data()

  • Removed clean_pop_data() function

  • Remove clean_pop_data() dependency functions documentation examples

  • Added age, value, id and standardize arguments to load_pop_data()

  • Added the following methods to pop_data class:

    • set_age()
    • set_value()
    • set_id_var()
    • get_age()
    • get_values()
    • ids()
    • get_age_var()
    • get_values_var()
    • ids_varname()

  • Added additional warnings to load_pop_data()

  • Added scales::pseudo_log_trans() to autoplot.pop_data() to avoid log 0

  • Added test-est.incidence-status.R test to check output when standardize option is FALSE on load_pop_data()

  • Replaced column name comparison on check_pop_data() to use attribute name on pop_data class

serocalculator 1.0.1

  • added n_points argument to plot_curve_params_one_ab()
  • Added type = "age-scatter" option for autoplot.pop_data()

serocalculator 1.0.0

  • Moved underlying methods to serocalculator vignette

serocalculator 0.5.0

  • Spell-checking of function documentation and tutorial articles.

  • Added functions and methods:

    • load_pop_data()
    • check_pop_data()
    • summary.pop_data()
    • autoplot.pop_data()
    • load_curve_params()

  • Renamed graph.decay.curves.by() to autoplot.curve_params()

serocalculator 0.4.0

  • plot() methods have been renamed to autoplot(), matching general convention for ggplot2-based graphics.

  • added visualization of curve parameters

  • sim.cs() now has format argument to specify long or wide format for output.

serocalculator 0.3.2

Fixed bug in passing antigen_isos from est.incidence.by() to est.incidence().

serocalculator 0.3.1

Rolled back required R version from 4.2 to 4.1

serocalculator 0.3.0

  • Fixed stability and documentation-clarity issues after initial tester feedback.

serocalculator 0.2.0 (never formally incremented in DESCRIPTION)

  • Added new vignettes.

serocalculator 0.1.0

Forking from the seroincidence package and adding Teunis et al 2020 approach.