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Changelog

Source: NEWS.md

EpiStrainDynamics 0.1.0

Breaking changes

  • construct_model()’s first two arguments are now pathogen_structure then method (previously method then pathogen_structure), to match the logical order in which a model is built: prepare the pathogen structure, then choose how to model it (#70). Any code calling construct_model() positionally (e.g. construct_model(my_method, my_pathogen_structure)) will need to swap the order of these two arguments; calls using named arguments are unaffected.
  • subtyped()’s influenzaA_unsubtyped_timeseries and influenzaA_subtyped_timeseries arguments are now unsubtyped_timeseries and subtyped_timeseries. The influenzaA_ prefix implied the structure only applied to influenza A subtypes, when it applies to any pathogen with a combined, unsubtyped timeseries alongside partial subtype data — influenza A is just the most common example (#73). Any code calling subtyped() with these named arguments will need to update the argument names.

Bug fixes

  • Fixed plot.incidence() hardcoding “Modelled influenza cases” as its y-axis label regardless of the pathogen(s) actually being modelled; it now reads the disease-agnostic “Modelled cases”.
  • Fixed the negative-binomial likelihood in the random-walk single-pathogen model when dow_effect = TRUE (#42).
  • Corrected the proportion() / plot() example in the vignette and fixed the underlying figure path so plots render correctly (#45).
  • Fixed the Rt() equation failing to render on the pkgdown site by setting MathJax as the math renderer (#44).
  • Fixed construct_model() and compute_multi_pathogen() erroring on R versions before 4.4.0 with “could not find function ‘%||%’”, by explicitly importing %||% from rlang instead of relying on base R’s version, which only exists from R 4.4.0 (related to #43).
  • Fixed intermittent R CMD check failures on Windows CI. The reported error (“Build process failed”) was misleading and had two distinct, unrelated causes hiding behind it, both only visible once compiler warning noise was suppressed (see below):
    • rstan’s own precompiled Windows binary DLL failed to load (“LoadLibrary failure”), most likely an ABI mismatch between the RSPM binary and the runner’s Rtools version. Fixed by reinstalling rstan from source on the Windows CI job specifically.
    • With that resolved, the package’s own compiled DLL then failed to load the same way, because StanHeaders:::LdFlags() unconditionally links against a dynamic tbb/tbbmalloc, which RcppParallel (from version 6.0.0) no longer reliably provides on Windows (having moved to static TBB linking), and -Wl,-rpath has no effect on Windows regardless. Fixed by dropping StanHeaders:::LdFlags() from src/Makevars.win’s PKG_LIBS and relying solely on RcppParallel::RcppParallelLibs(), matching what rstan’s own Windows build does. Also lowered optimisation from -O2 to -O1, suppressed compiler warnings, and enlarged the Windows runner’s pagefile in src/Makevars.win/CI config; these weren’t the actual fix for either issue above, but remain in place as they reduce build time/noise and are otherwise harmless.

Minor improvements

  • proportion() now returns the resolved pathogen names used as its numerator and denominator ($numerator_combination / $denominator_combination), and plot.proportion() adds a subtitle reporting the denominator when it isn’t the default (all pathogens), since the denominator otherwise has no representation anywhere on the plot (#69).
  • Capped the viridis palette used by plot() methods at end = 0.9 so the palest yellow no longer makes lines hard to distinguish (#71).
  • Plot functions now call ggplot2 functions explicitly rather than importing the whole package (#35).
  • Standardised quotation-mark style (#37).
  • Reordered function arguments so those without defaults precede those with defaults (#38).
  • Enabled parallel testing with Config/testthat/parallel: true (#39).
  • Added tests for MCMC validation.
  • Added a print() method for EpiStrainDynamics.model objects (#47).
  • Standardised error handling on cli::cli_abort() (#49).
  • plot() is no longer redefined as a generic (#48), and its S3 methods’ first argument was renamed from df to x to match the base generic’s signature, resolving an R CMD check S3 generic/method consistency warning.
  • Increased the minimum R version to 4.1.0, matching actual base pipe usage, and added it to the R-CMD-check.yaml test matrix (#43).
  • Fixed all lintr-identified issues (#50): styling (line length, indentation, spacing) via styler, dropped explicit return() on final statements, converted sapply() to vapply() for type-safe extraction, and removed genuine dead code flagged by unused-variable checks.

Documentation

  • Replaced \dontrun{} in examples with @examplesIf interactive() for slow examples and guards such as @examplesIf rlang::is_installed("xts") where a package is used only in an example (#36).
  • Expanded documentation for Rt(), including its gi_dist argument (#44).
  • Expanded documentation for smoothing_structure() and diagnose_model() (#53, #54).
  • Expanded documentation for growth_rate(), incidence(), and proportion() to match the level of detail in Rt(), including symbol breakdowns for their adjustment formulas and, for growth_rate(), its relationship to Rt() (#66).
  • Added roxygen [] cross-links for referenced functions throughout the documentation (#55).
  • Committed precompile.R for the vignette and included revision instructions in CONTRIBUTING.md (#46).
  • Clarified contribution and maintenance guidelines, added installation- from-source instructions, and added citations to the README (#51, #57, #58, #59, #60).
  • Corrected documentation of both sarscov2 and influenza datasets (#56).
  • Added explanations of “pathogen noise” and the day-of-week effect (#61), a link to the relevant timeseries class (#62), and a COVID-19 example (#63), to the vignette.
  • Clarified the G1.6 srr standard statement to note that, although performance/scaling is evaluated in the vignettes, this does not constitute an explicit comparison against alternative implementations (#52).

EpiStrainDynamics 0.0.1 (2026-03-27)

Initial version submitted to rOpenSci for peer review (ropensci/software-review#763).

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