serodynamics 0.1.0

This is the first CRAN release of serodynamics, a package for Bayesian hierarchical modeling of antibody kinetics from longitudinal serological data. It serves as the upstream companion to the serocalculator package.

New features

• Reorganized pkgdown documentation with new “Getting Started” guide demonstrating main API workflow, organized articles into “Get started” and “Developer Notes” sections (#73).
• Made “newperson” optional in prep_data() (#73)
• Including fitted and residual values as data frame in run_mod output. (#101)
• Added plot_predicted_curve() with support for faceting by multiple IDs (#68)
• Replacing old data object with new run_mod output (#102)
• Adding class assignment to run_mod output (#76)
• Making prep_priors modifiable (#78)
• Changes to run_mod() output:
  • Taking out include_subs as an input option, default will include all individuals
  • Making a single tbl as output
  • All other pieces will be attributes.
• Changes to run_mod() (#79):
  • jags.post now optionally included in output, as specified by argument with_post
  • all subjects now optionally included in curve_params output component, as specified by argument include_subs
• Diagnostic function to produce R-hat dotplots with stratification (#67)
• Added function for summarizing estimates in a table (#74)
• Diagnostic trace plot function with strat (#64)
• Diagnostic function to produce effective sample size plots with stratification (#66)
• Diagnostic function to produce density plots with stratification (#27)
• Added SEES data set data folder and documentation (#41)
• Fixing SEES data and added jags_post for SEES (#63)
• as_case_data() now creates column visit_num (#47, #50)
• Added postprocess_jags_output() to API (#33)
• Added initsfunction() to API (#37)
• Added participant IDs as names to nsmpl element of prep_data() output (#34)
• Added initsfunction() to API (#37)
• Added as_case_data() to API (#31)
• Added prep_priors() to API (#30)
• Added autoplot() method for case_data objects (#28)
• Added examples for sim_pop_data(), autoplot.case_data() (#18)
• Added attributes as a return to the run_mod function (#24)
• exported run_mod() function (#22)
• Function that runs jags with option of stratification included. (#14)
• Changed package name to serodynamics. (#19, #20)

Bug fixes

• Fixed dplyr::as_tibble() references to tibble::as_tibble() in post_summ() and run_mod(), since as_tibble() is exported from the tibble package, not dplyr.

Developer-facing changes

• Expanded what the Claude Code (@claude) workflow can do:
  • Install the full R toolchain (R, JAGS, pandoc, the apt system libs mirrored from copilot-setup-steps.yml, plus devtools, roxygen2, rmarkdown, lintr, spelling, rcmdcheck) and allow Rscript, R, and R CMD invocations, so requests that need package- maintenance commands (devtools::document(), spelling::spell_check_package(), R CMD check, vignette rebuilds) succeed instead of being patched by hand.
  • Grant issues: write and allow gh issue invocations so Claude can file follow-up issues for work deferred out of the current PR instead of burying it in a comment.
• Standardized runjags::findjags() casing across test-coverage.yaml and copilot-setup-steps.yml to match the R-CMD-check.yaml form arriving with the 0.1.0 release (#207 advisory).
• Re-assign reviewers to a PR’s human assignees (filtered via type == "User") when Claude pushes commits during a @claude or Claude Code Review run; if Claude makes no commits, the original reviewer set is restored as before. Detected by comparing the PR’s head SHA before and after the Claude step (#210).
• Stopped deleting prior Claude review comments at the start of each Claude Code Review run, so reviews posted by @claude review invocations are preserved across subsequent pushes instead of being wiped when the review step fails its bot-actor gate (#217).
• Hardened the Claude code-review workflow against races and silent failures: serialized concurrent runs per PR, made reviewer restore fail loudly instead of silently dropping reviewers, and cleaned up all stale Claude top-level comments per run (#216).
• Consolidated OS-specific snapshot variants: removed redundant Linux and Windows snapshot directories (which were identical), keeping only base snapshots and darwin-specific variants for macOS platform differences (#73).
• Updated Copilot instructions to encourage code decomposition and avoid copy-pasting substantial code chunks.
• Expanded .github/copilot-instructions.md with additional guidance on evidence-based claims, Quarto markdown/cross-reference conventions, R style practices, and phrase-level line-break formatting for source text.
• Added R 4.5+ snapshot variants to handle the changed attribute ordering in as_case_data(), ensuring test suite compatibility with R 4.5 and later (#109).
• Added dev container configuration for persistent, cached development environment that includes R, JAGS, and all dependencies preinstalled, making Copilot Workspace sessions much faster.
• Added .github/workflows/copilot-setup-steps.yml GitHub Actions workflow to automate environment setup for GitHub Copilot coding agent, preinstalling R, JAGS, and all dependencies.
• Switched ggmcmc dependency from GitHub dev version to CRAN v1.5.1.2 (#135)
• vectorized ab() function (#116)
• Added lintr::undesirable_function_linter() to .lintr.R (#81)
• Reformatted .lintr as R file (following https://github.com/r-lib/lintr/issues/2844#issuecomment-2776725389) (#81)
• Set shortcut pipe to be base pipe (#80)
• Added snapshot test for run_mod()
• Clarified prep_data() internals using {dplyr} (#34)
• Removed “.R” suffix from jags model files to prevent them from getting linted as R files (#34)
• Added dobson.Rmd minimal vignette (#36)
• Overall cleaning to get checks working (#28)
• Added units tests for prep_data(), sim_case_data() (#18)
• Added various GitHub Actions (#10, #15, #18)

serodynamics 0.0.0

Started development.