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Changelog

Source: NEWS.md

jsurvival 1.0.0 (2026-07-13)

First stable release

  • Fixed both odds-ratio validation paths so empty or invalid data produce clear analysis-level errors instead of an R6 method failure.
  • Replaced non-structural named HTML entities with Unicode and converted fragmented translated output to complete placeholder-based sentences.
  • Normalized checkbox labels to noun phrases, removed stale sas invalidation keys, and hid unfinished survival-tree controls until the feature is wired end to end.
  • Trimmed 00refs.yaml to the 22 citations used by the eight analyses and replaced broad package imports with selective imports.
  • Synchronized DESCRIPTION, jamovi metadata, and CITATION.cff; removed the orphaned survival-power event handler.

jsurvival 0.0.47 (2026-07-05)

Bug Fixes

  • Fixed a crash in competing-risks analysis on jamovi installs. cmprsk::cuminc() is called by the survival, single-arm, continuous-survival, and multivariable-survival analyses, but cmprsk was missing from the package Imports. Because jamovi installs only a package’s Imports, competing-risks analysis failed on a clean install with “there is no package called ‘cmprsk’”. cmprsk is now declared.
  • Declared digest, pec, and rpart.plot (previously used via :: but undeclared). Moved the optional machine-learning survival backends (randomForestSRC, xgboost, survivalsvm, SurvMetrics) to Suggests so they degrade gracefully when not installed.

jsurvival 0.0.46 (2026-07-04)

This release consolidates versions 0.0.32.62 through 0.0.46 into a single entry. Headline themes: a major expansion of the univariate Survival module toward REMARK-compliant prognostic reporting (age-adjusted analysis, a weighted log-rank test family, calibration assessment, non-linearity testing, and bootstrap internal validation); Cox interaction / effect-modification terms in Multivariable Survival; Firth penalized logistic regression in Odds Ratio; and a unified multi-tier HTML notice system across modules. Minimum jamovi version raised to 2.7.27.

New Statistical Features

Univariate Survival (survival)

  • Age-adjusted survival analysis — new option group controlling age adjustment (age_adjustment, age_variable):
    • age_interaction — test an age x group interaction (new ageInteractionTable with coefficient, HR, SE, z, p-value).
    • age_stratified_cox and ageAdjustedCoxTable comparing unadjusted vs. age-adjusted hazard ratios side by side.
    • age_time_scale — fit a Cox model using age as the time scale (new ageTimeScaleTable).
    • age_standardization with age_standardization_method (indirect/SMR or direct) producing an ageStandardizationTable (observed/expected deaths, SMR with 95% CI).
    • age_stratified_km and age_group_cutpoints for age-stratified Kaplan-Meier curves (ageStratifiedKMPlot).
    • adjusted_curves — covariate-adjusted survival curves (adjustedCurvesPlot).
    • Interpretation panels: ageAdjustedInterpretation, ageAdjustedExplanation, ageTimeScaleInterpretation, ageStandardizationInterpretation.
  • Weighted log-rank test family — new weightedLogRank option with survivalTestType choices: logrank, gehan_breslow, tarone_ware, peto_peto, and fleming_harrington; results in weightedLogRankTable (test, rho, chi-square, df, p-value, weighting) plus a weightedLogRankExplanation panel. Pairwise group comparisons now honor the selected rho weighting.
  • Calibration assessment — calibration_curves with calibration_timepoint and calibration_ngroups; outputs calibrationTable, per-group calibrationGroupTable (predicted vs. observed with CIs), calibrationPlot, and calibrationInterpretation.
  • Non-linearity assessment (restricted cubic splines) — rcs_analysis with rcs_variable and rcs_knots; outputs rcsTestTable (model, df, log-likelihood, AIC, LR chi-square, p-value, conclusion), rcsPlot, and rcsInterpretation.
  • Bootstrap internal validation — bootstrapValidation with bootstrapValN resamples; bootstrapValidationTable reports apparent, optimism, and optimism-corrected metrics with a bootstrapValidationExplanation.
  • REMARK reporting checklist — remark_checklist option renders a remarkChecklist HTML panel for prognostic-marker reporting.
  • Parametric survival scaffolding — UI options added (use_parametric, parametric_distribution covering exponential, Weibull, log-normal, log-logistic, gamma, generalized gamma, Gompertz, and Royston-Parmar spline; spline_knots, spline_scale, parametric_covariates, parametric_extrapolation, extrapolation_time, parametric_diagnostics, compare_distributions, parametric_survival_plots, hazard_plots). The parametric backend remains disabled/experimental in this release.

Multivariable Survival (multisurvival)

  • Cox interaction / effect-modification terms — new interactions option (type Terms) that crosses variables already chosen as explanatory or continuous-explanatory predictors.
    • New interactionTest table (interaction HR with 95% CI and p-value) and subgroupHR table (within-subgroup hazard ratios by moderator level).
    • New pure, unit-testable helper module R/multisurvival-interactions.R (term mapping, formula construction, moderator/subgroup summaries), separated from the R6 backend for maintainability.
    • New jamovi/js/multisurvival.events.js model-builder events that populate the interaction predictor pool from the explanatory/contexpl boxes and prune stale terms.

Odds Ratio (oddsratio)

  • Firth penalized logistic regression — new usePenalized option (via logistf) to reduce small-sample bias and handle separation, with profile-likelihood confidence intervals and automatic fallback to standard logistic regression when logistf is unavailable.
  • New predictorLevel option to set the positive level of the predictor.

Enhanced Existing Modules

Multivariable Survival (multisurvival)

  • Proportional-hazards testing (ph_cox) now defaults to on, surfacing global and per-covariate Schoenfeld residual statistics via survival::cox.zph (aligned with REMARK reporting guidance).

DateTime Converter (datetimeconverter)

  • Added a unified HTML notices panel for validation and conversion messaging.

Notices & Messaging System

  • Introduced a four-tier structured HTML notice system (errors, strongWarnings, warnings, infoMessages) with .addHtmlMessage() / .initializeMessageOutputs() helpers, wired into survival, multisurvival, oddsratio, and outcomeorganizer. Message outputs are reset at the start of each run to prevent accumulation across runs.

Module Removals

  • Removed the Date/DateTime Validator (datevalidator) module (backend, header, and all .a/.r/.u.yaml files deleted).

Package Infrastructure

  • Raised the minimum jamovi application version (minApp) from 1.8.1 to 2.7.27.
  • Added internal helper library R/diagnostichelpers.R with diagnostic-accuracy functions (sensitivity, specificity, PPV/NPV with optional prevalence/Bayes adjustment, positive/negative likelihood ratios, diagnostic odds ratio, Youden’s J).
  • Added internal helper library R/survivalPower_distributions.R implementing Weibull, log-normal, and piecewise-exponential parameterizations and expected-events calculations (Lachin & Foulkes reference).
  • Expanded dataset roxygen documentation in R/data.R (histopathology, melanoma, longitudinal, and stage-migration test datasets).
  • Reworked reproducible-syntax generation (asSource) and hardened R-string escaping across module functions. R/utils.R gains new formula helpers (.asSurvivalFormula(), .escapeVariableNames(), .buildSurvivalFormula()) and %notin%/%!in% operators so that variable names containing special characters produce valid Syntax-mode output.
  • Hardened error handling in Time Interval Calculator (timeinterval) with additional jmvcore::reject() guards for invalid or missing dates and unsupported date formats.
  • Updated bibliographic references in jamovi/00refs.yaml.

jsurvival 0.0.32.60 (2025-12-28)

Major Updates

New Modules

  • Date Validator: Comprehensive date and datetime validation tool.
    • Validates and diagnoses messy date/datetime formats using multiple methods (datefixR, anytime, lubridate).
    • Provides detailed audit tables and quality assessment reports.

Re-introduced and Enhanced Modules

  • Outcome Organizer: Re-introduced with significant enhancements.
    • Improved data cleaning and label handling.
    • Contextual validation for different survival analysis types (OS, Cause-specific, etc.).
    • Diagnostic messages and glossary for educational support.
  • Time Interval: Re-introduced as a comprehensive calculator.
    • Robust time interval calculations with landmark analysis support.
    • Person-time calculation for epidemiological studies.
    • Data quality assessment for time intervals.

Enhancements

Survival Analysis

  • Parametric Models: Improved handling of covariates and formula construction.
  • Plots: Added logic to skip certain plots (e.g., PH assumption, residuals) for competing risk analysis to avoid errors.
  • Diagnostics: Enhanced model summaries and p-value calculations.

General

  • Notice System: Improved notice generation and handling across modules.
  • Documentation: Updated documentation for all modules.

jsurvival 0.0.31.84 (2025-10-03)

New Features

Educational Explanations

  • Added showExplanations option to survival, survivalcont, multisurvival, and oddsratio modules
  • Built-in HTML explanations for key analysis concepts and statistical methods
  • Context-sensitive educational content to help users understand their analyses

Single Arm Survival Enhancements

  • Clinical Analysis Presets: Pre-configured settings for common study types
    • Overall survival analysis (most common)
    • Disease-free survival analysis
    • Treatment effectiveness study
    • Post-surgical outcomes
    • Custom analysis (advanced users)
  • Guided Setup Mode: Step-by-step guidance for users new to survival analysis
  • Enhanced person-time calculations and natural language summaries

Stage Migration Analysis

  • Advanced TNM staging validation and trend analysis
  • Improved robustness and explanations for stagemigration module
  • Multifactorial analysis capabilities
  • Granular table controls and debug outputs

Survival Analysis Module

  • Enhanced educational explanations for univariate survival
  • Improved Cox regression output and interpretation
  • Additional visualization options

Continuous Survival Analysis

  • Educational explanations for cut-point analysis
  • Enhanced optimal threshold determination methods
  • Improved output tables and visualizations

Multivariable Survival

  • Educational explanations for multivariable models
  • Enhanced model diagnostics and output

Odds Ratio Analysis

  • Educational explanations for odds ratio interpretation
  • Improved forest plots and summary tables

Module Removals

  • Removed outcomeorganizer module (functionality integrated into other modules)
  • Removed timeinterval module (functionality integrated into other modules)

Bug Fixes and Improvements

  • Enhanced diagnostic test utility functions
  • Improved tree analysis for survival models
  • Better handling of missing data
  • Updated documentation across all modules

Documentation

  • Updated package documentation and vignettes
  • Enhanced inline help and tooltips
  • Improved example datasets and use cases

jsurvival 0.0.3.90 (2024-07-31)

Major Changes

  • Initial implementation of educational explanations system
  • Refactored analysis modules for better user experience
  • Enhanced natural language summary generation

New Features

  • Stage migration analysis for cancer staging studies
  • Advanced survival model options
  • Diagnostic test utility functions

jsurvival 0.0.3.0 and earlier

For changes in earlier versions, please refer to the git commit history.