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Changelog

Source: NEWS.md

siera 0.5.6

CRAN release: 2026-06-17

  • Added formatted results to generated ARDs. Each ARD row now carries res (the raw statistic flattened to numeric), pattern (the ARS resultPattern for the row’s operation) and disp (the printable, table-ready formatted value, e.g. (N=86), honouring the pattern’s decimal count and prefix/suffix). cards proportions (stat_name == "p") are multiplied by 100 before formatting, matching the percentage semantics of result patterns. Rounding follows the clinical-reporting norm of rounding halves away from zero (the SAS ROUND() convention, e.g. 1.369 becomes 1.4 and 2.5 becomes 3) rather than R’s default round-half-to-even, so disp aligns with SAS-generated reference tables; the raw res value is left unrounded. The cards-internal fmt_fun/fmt_fn format-function list-columns, which previously surfaced as unprintable values, are dropped from the final ARD (#167).
  • Added support for resolving a method’s code template from an external reference instead of inline ARS metadata. When a method’s codeTemplate carries a documentRef (rather than inline code), readARS() now follows the ARS referenceDocuments chain to load the template - and, where the method declares none inline, its parameters - from either a siera method manifest (a .json superset of method.json carrying templateCode + parameters, with a method selected by a pageRefs named destination = the method id) or a bare .R/.txt code file. Resolution is transparent: a documentRef ARS generates the same script as its inline equivalent. The whole method library now also ships as one referenceable catalog, inst/method-library/method-library.json, and new bundled examples (exampleARS_5_documentref.json/.xlsx + exampleARS_methods.json) demonstrate the mechanism. v1 resolves local paths only (relative to the ARS file, or absolute); remote URLs are rejected. JSON and XLSX inputs are supported with parity (via the XLSX ReferenceDocuments and AnalysisMethodDocumentRefs sheets) (#175).
  • Added method_library(), an exported accessor that lists the bundled analysis-method templates and resolves a method’s files on disk (parallel to ARS_example()).
  • Added a plain-text, testable analysis-method template library under inst/method-library/ (one method.json + template.R per method, plus a reconciled constructs.json valueSource registry and a generated METHODS.md catalog). This becomes the reviewable, diff-able source of truth for the code-template recipes that drive ARD generation; its method ids are intended as stable keys an ARS file can reference. A contract test validates every recipe on each run (templates parse, only supported valueSources are referenced, no orphan tokens, no duplicated case_when mappings, and the human-readable catalog stays in sync). Introduced an internal .supported_value_sources() helper as the declared valueSource contract. The legacy inst/extdata/R_siera_codes.xlsx and cards_constructs.xlsx are left untouched (#173).
  • Added support for per-category risk differences. A new method template computes one risk difference and 95% confidence interval for each data-driven inner category (e.g. one per preferred term or system organ class) by looping over the second grouping and calling cardx::ard_stats_prop_test() within each, instead of collapsing the analysis to a single overall risk difference (#157).
  • Added per-category risk differences for pre-defined (non-data-driven) inner groupings. A new method template, risk_difference_per_predefined_group, honours the groups declared in the ARS metadata instead of looping observed data values: every defined group is emitted - a group whose condition matches no events yields a risk difference of 0 with a [0, 0] confidence interval - and data values matching no defined group are excluded. It is driven by a new AG_var2_group_values valueSource that resolves the second grouping’s group condition values, in group order (single-value EQ conditions; other comparators are skipped with a warning). Validated on the eTFL “Overview of Adverse Events” table (one risk difference per action taken and per severity) against an independent stats::prop.test() recomputation; the published reference matches on category shape and empty groups, but its non-zero values were found to be computed from only the first adverse-event record per subject rather than from all qualifying events, so they are not used as the value oracle (#171).
  • Added per-(category x category) risk differences for analyses with two data-driven inner groupings, such as one risk difference per system organ class and preferred term combination. A new method template, risk_difference_per_group_pair, loops the distinct combinations of the second and third grouping variables observed in the analysis subset, computes each risk difference with cardx::ard_stats_prop_test(), and stamps both category levels onto the ARD rows. It reuses the existing AG_var3 valueSource, so no change to readARS() was required. Validated on the eTFL “Adverse Events by System Organ Class and Preferred Term” table against an independent stats::prop.test() recomputation over every observed combination (#172).
  • Fixed zero-event risk-difference analyses returning NA instead of 0. Methods that compute over the full population (templates referencing df_poptot, e.g. risk differences) now bypass the empty-data subset guard, so an analysis with no events emits the conventional risk difference of 0 with a [0, 0] confidence interval (#156).
  • Accepted SAS transport (.xpt) ADaM datasets in addition to CSV. readARS() chooses the reader for each ADaM dataset from its file extension (.csv via readr::read_csv(), .xpt via haven::read_xpt()), with no new argument; the file lookup is case-insensitive so lower-case submission file names (e.g. adsl.xpt) match upper-case ARS dataset names. Reading .xpt requires the haven package.
  • Fixed readARS() crash when ARS metadata contains no referencedAnalysisOperations (continuous-only tables such as shift tables) by ensuring accumulator frames are initialised with their merge key columns.
  • Normalised Windows backslashes in ADaM file paths to forward slashes so generated scripts run correctly on both Windows and Unix systems.
  • Added CDISC ARD-compliant column stamping: generated scripts now write group[n]_groupingId, group[n]_groupId (for pre-defined groups) and group[n]_groupValue (for data-driven groupings) onto each ARD row.
  • Supported arbitrarily deep nesting in mainListOfContents via a recursive LOPA extraction helper, removing the previous three-level hard limit.
  • Expanded support for multi-value ARS group conditions (IN/NOTIN) by unnesting condition.value list columns in the JSON parser.
  • Coerced *_level columns to character on each individual ARD frame before bind_rows, preventing type conflicts between continuous and categorical analyses.
  • Allowed more than three grouping factors per analysis.
  • Updated bundled cards_constructs.xlsx example file and extended test coverage across metadata parsing, ADaM loading, and ARD script generation.

siera 0.5.5

CRAN release: 2025-12-01

  • Strengthened analysis method validation with clear errors for missing or undefined MethodId values and warnings when method templates or parameter value sources cannot be resolved.
  • Added guardrails for analysis set generation that warn on missing or incomplete metadata and fall back to the unfiltered analysis dataset when needed.
  • Tightened ARS metadata ingestion by requiring analysisSets definitions in JSON and the analysis code template sheets in Excel workbooks.
  • Expanded test coverage for analysis methods, analysis sets, and data subset condition handling to capture more metadata edge cases.

siera 0.5.4

CRAN release: 2025-09-25

  • Comprehensive testing added: checking generated ARD result values
  • added warning messages with cli()
  • cover scenarios for bigN vs table-level subsetting

siera 0.5.3

CRAN release: 2025-08-28

  • Cover scenario of multi-value DataSubsets
  • Cover scenario of overlapping variables in ADSL merge

siera 0.5.2

CRAN release: 2025-08-25

  • Added conditional operators to cover EQ, NE, GE, GT, LE, LT

siera 0.5.0

CRAN release: 2025-07-29

  • readARS function to ingest xlsx, json and CDISC example

siera 0.4.0

CRAN release: 2025-07-18

  • addition of readARS_xl function
  • example added of {cards} in AnalysisMethodCodeTemplate

siera 0.3.0

CRAN release: 2025-03-03

  • dynamic recognition of ADaMs

siera 0.1.0

CRAN release: 2025-02-10

  • Initial CRAN submission.