Changelog

Source: NEWS.md

serodynamics (development version)

• Initial CRAN submission.

New features

• 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)

serodynamics 0.0.0

Started development.