serocalculator (development version)

Internal

  • Render documentation vignettes as HTML only for the altdoc website (removed leftover revealjs/pptx output formats from vignettes/_metadata.yml and simulate_xsectionalData.qmd), fixing a quarto output-filename collision that broke the docs build. (#503)
  • 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)

Bug fixes

  • 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

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

  • 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

  • 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.