serocalculator 1.4.1

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

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().
• Fixed errors coming from parallel processing in examples flagged by CRAN checks using \donttest

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 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:

  • check that README.qmd still compiles
    (advice from preventive-r-package-care) (#259)
  • check NEWS.md for updated change log (#257)
  • lint changed files (#256)