Changes in version 0.0.0.9055 - Clarified Code Style Guidelines in .github/copilot-instructions.md: the UCD-SeRG Lab Manual takes precedence over the tidyverse style guide where they conflict, and functions should end with an explicit return() call per the lab manual / Google R Style Guide. This closes a gap where @claude reviews were flagging explicit returns as non-conforming. - 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). - 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. - 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. - 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. - Reorganized pkgdown documentation with new "Getting Started" guide demonstrating main API workflow, organized articles into "Get started" and "Developer Notes" sections (#73). - 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. - Added reference to UCD-SeRG Lab Manual in copilot-instructions for lab-wide best practices guidance. - 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). - Initial CRAN submission. - Updated Copilot instructions to encourage code decomposition and avoid copy-pasting substantial code chunks. New features - Including optional population parameters as attributes in run_mod output. (#141) - 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 None yet Developer-facing changes - 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) Changes in version 0.0.0 Started development.