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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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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