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Changelog

Source: NEWS.md

serodynamics (development version)

  • Implemented multi-version documentation with dropdown menu for package versions, based on insightsengineering/tern setup. Documentation is now versioned by tags and branch, with the latest release as the default landing page.

  • 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.

  • 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

  • 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

serodynamics 0.0.0

Started development.