Changes in version 6.5.3-1.0.1 (2026-06-12)               

Breaking: split parameter bundles (shg-params)

  - Removed params_bundle_source and single-zip shg_load_params(url =
    ...).
  - Required separate smoking and mortality releases:
    smok_params_source, mort_params_source, and mort_params_type ("acm"
    or "ocm"; was params_mortality).
  - shg_load_params() downloads/caches each zip, merges params/ tables
    into engine layout smoking/ + mortality/.
  - Portable YAML and getConfig() / getReproConfig() use the new
    provenance field names.

                     Changes in version 6.5.3-1.0.0                     

  - Synced core engine from shg-cli v6.5.3.
  - Windows: open bundled CSV tables in binary mode so ftell/fseek
    dimension scans work; strip CR/LF on all CSV lines in CPD,
    initiation/cessation, and mortality loaders so missing "." fields
    parse correctly with CRLF.

                     Changes in version 6.5.2-1.0.0                     

Bundled inputs and YAML

  - Bundled inputs: Default factory input_data_folder is
    system.file("extdata", "2018", package = "SmokingHistoryGenerator")
    (NHIS-1965–2018 csv-partial with cohort columns 1940, 1950, 2010).
    Removed transitional inst/extdata/2016/, NHIS-1965–2016 test
    fixtures, and tests/fixtures/2016/ XML goldens; tests and docs use
    the 2018 tree only. Regenerate the 2018 partial from
    tests/testdata/NHIS-1965-2018/csv-complete/ using Rscript
    tools/refresh-nhis-2018-csv-partial.R.
  - Layout: Under each year folder, smoking tables live in smoking/,
    mortality in mortality/; factory defaults use relative paths
    (smoking/initiation.csv, …).
  - Portable / written YAML groups params_bundle_source,
    params_mortality, and optional folder paths under a params: map;
    shg_load_config / shg_apply_config accept nested or flat keys.

Reproducibility

  - getReproConfig() / portable YAML omit num_threads (effective segment
    count and seeds define the run; thread count defaults to auto on
    reload).
  - getReproConfig() exports package_repro as r_package_version only
    (full install metadata remains internal for fingerprint checks).
  - Run bundles with attach_run_info = TRUE enrich repro_config with a
    nested results block (content_md5, compact summary) and a single
    repro_digest (engine settings plus R session). Legacy flat results_*
    / repro_engine_md5 / r_session_md5 keys in YAML are merged or
    dropped on load.
  - Summaries omit sentinel -999; age_at_death is split for never vs
    ever death-age stats (mean, sd, n_obs). Top-level ever_smokers holds
    count, fraction, and integer cpd_mode (most common rounded CPD among
    ever smokers). Keys count (never/ever totals) and n_obs (rows
    contributing to each mean/sd) replace bare n (YAML 1.1 reserves n).
    Initiation and cessation means use ever smokers only;
    age_at_death$ever_smokers is only death-age statistics (not the same
    list as top-level ever_smokers).
  - shg_save_config(..., results = ) optionally writes those
    verification fields (including content_md5 and compact results
    summary metadata when results is supplied).

Configuration

  - CLI sync metadata: src/shg-cli-info.txt (YAML map shg-cli: with
    MostRecentTag, CommitHash, SrcHash; listed in .Rbuildignore so it is
    not shipped in CRAN source tarballs); python tools/shg-sync.py
    update-description refreshes it from the sibling shg-cli checkout. R
    merges these into the packageDescription() list as SHGMostRecentTag,
    SHGCommitHash, and SHGsrcHash when the file is present (for example
    devtools::load_all() from a checkout). The old RWrapperVersion field
    is dropped.

  - shg_load_params() (URLs): shg.params.download.timeout_sec
    (default 600) and shg.params.download.connect_sec (default 60) when
    httr2 is installed; clearer HTTP/network errors; HTML and non-zip
    responses detected before unzip.

  - shg_reset_defaults() / shg$reset_to_factory_defaults() restore
    engine fields to the same defaults as a fresh SHGInterface.

  - shg_apply_config(shg, config) resets defaults, then applies a sparse
    or full named list via useConfig(), so partial YAML/intent configs
    do not inherit stale instance state.

  - shg_apply_config() with params_bundle_source now calls
    shg_load_params() the same way as shg_load_config() (clears derived
    paths, restores the bundle). Without a bundle, explicit
    input_data_folder / table filenames in the list are still applied.

  - shg_load_config() now starts from factory defaults before applying
    the YAML bundle (via reset_to_factory_defaults() in the bundle
    applier).

  - shg_write_config_yaml(config, path) serializes any config list:
    drops audit keys, and strips redundant table paths when
    params_bundle_source is present (shape-driven “portable” output).

  - Config lists and YAML may use mortality as an alias for
    params_mortality. Normalization uses [[ only so it does not
    partially match mortality_filename.

  - Factory defaults: mortality file is mortality/acm.csv, matching
    shg_load_params(..., mortality = "acm") bundle layout.

Simulation return value

  - shg$runSimFromFixedValues(..., attach_run_info, original_config) and
    shg$runSimFromDataFrame(..., attach_run_info, original_config)
    (6-argument forms): when attach_run_info is TRUE, the return value
    is a list with results, original_config (sparse intent; default for
    fixed cohort = repeat/race/sex/cohort_year), repro_config (post-run
    getReproConfig(FALSE)), and run_info (host/software/audit).
  - The 4- and 1-argument forms keep the previous behavior: a data.frame
    of simulation output (attach_run_info = FALSE).
  - shg_run() / shg$runSim() accept attach_run_info (default TRUE; set
    FALSE for data-frame-only return).
  - shg_run() / shg$runSim(): if repeat, individuals, and N are all
    omitted, repeat defaults to 1000.

Note

Direct shg$useConfig() without shg_apply_config() still overlays on the
current instance (legacy). Prefer shg_apply_config() for defaults-first
semantics.