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Changelog

Source: NEWS.md

meddecide 0.0.47 (2026-07-05)

Bug Fixes

  • Restored correct inter-rater agreement statistics on jamovi installs. vcd and lme4 are used by agreement() but were missing from the package Imports. Because jamovi installs only a package’s Imports, on a clean install they were unavailable: pairwise kappa confidence intervals silently fell back to the narrower irr::kappa2 null-SE method, and the entire ICC / Lin’s CCC / continuous-agreement suite (which relies on lme4) was non-functional. Both are now declared, so agreement CIs use the intended vcd::Kappa asymptotic-SE method and the continuous-agreement measures work.
  • Clarified the all-pairs kappa fallback note so it distinguishes a missing vcd package (with install guidance) from a genuinely near-degenerate table.
  • Declared DescTools and lmerTest, previously used via :: but undeclared.

meddecide 0.0.46 (2026-07-04)

This release consolidates every change since 0.0.32.69 (unreleased versions 0.0.33 through 0.0.46 roll into this entry). The headline is a large expansion of agreement() into a comprehensive interrater/intrarater reliability suite (20+ new agreement statistics, tests, and visualizations), robustness and input-validation hardening of the ROC modules, one-sided confidence-interval support in the kappa sample-size tools, and package infrastructure updates (minimum jamovi app raised to 2.7.27, new imports, dataset cleanup).

Major Changes

agreement() — Comprehensive Reliability Suite Expansion

The agreement module was expanded from Cohen’s/Fleiss’ Kappa into a full interrater/intrarater reliability toolkit. Each new statistic ships with its own results table, an “About …” HTML explanation, and a “When to use …” guide notice.

  • New chance-corrected / categorical measures:
    • Gwet’s AC1/AC2 (gwet, with gwetWeights: unweighted/linear/quadratic) → gwetTable
    • PABAK with prevalence and bias indices (pabak) → pabakTable
    • Light’s Kappa for 3+ raters (lightKappa) → lightKappaTable
    • Krippendorff’s Alpha guidance (showKrippGuide)
  • New continuous-data agreement measures:
    • ICC with six models ICC(1,1)–ICC(3,k) (icc, iccType) → iccTable
    • Mean Pearson correlation (meanPearson) → meanPearsonTable
    • Lin’s Concordance Correlation Coefficient (linCCC) → linCCCTable
    • Total Deviation Index (tdi, tdiCoverage, tdiLimit) → tdiTable
    • Finn coefficient with one-way/two-way models (finn, finnLevels, finnModel) → finnTable
    • Iota multivariate coefficient (iota, iotaStandardize) → iotaTable
  • New ordinal / rank-based agreement measures:
    • Kendall’s W coefficient of concordance (kendallW) → kendallWTable
    • Robinson’s A ordinal agreement index (robinsonA) → robinsonATable
    • Mean Spearman rho (meanSpearman) → meanSpearmanTable
  • New marginal-homogeneity / rater-bias tests:
    • Rater Bias test (raterBias) → raterBiasTable
    • Bhapkar test (bhapkar) → bhapkarTable
    • Stuart-Maxwell test (stuartMaxwell) → stuartMaxwellTable
    • Maxwell’s RE random-error index (maxwellRE) → maxwellRETable
  • New multi-rater / structural analyses:
    • Pairwise Kappa against a reference rater with performance ranking (pairwiseKappa, referenceRater, rankRaters) → pairwiseKappaTable
    • Hierarchical/multilevel Kappa (hierarchicalKappa, clusterVariable) with cluster-specific estimates, variance-component decomposition, hierarchical ICC, cluster-homogeneity test, and shrinkage (empirical Bayes) estimates → hierarchicalOverallTable, clusterSpecificTable, varianceDecompositionTable, hierarchicalICCTable, homogeneityTestTable
    • Mixed-effects condition comparison with Bonferroni/BH/Holm correction (mixedEffectsComparison, conditionVariable, multipleTestCorrection) → mixedEffectsTable, mixedEffectsVarianceTable
    • Inter/intra-rater test-retest reliability (interIntraRater, interIntraSeparator) → interIntraRaterIntraTable, interIntraRaterInterTable
  • New machine-learning-style metrics:
    • Confusion matrix table with row/column normalization (confusionMatrix, confusionNormalize) → confusionMatrixTable, perClassMetricsTable
    • Multi-annotator concordance / F1 (multiAnnotatorConcordance, predictionColumn) → concordanceF1Table, concordanceF1PerClassTable
    • Specific (category-focused) agreement indices with optional CIs (specificAgreement, specificPositiveCategory, specificAllCategories, specificConfidenceIntervals) → specificAgreementTable
    • Bootstrap confidence intervals (bootstrapCI, nBoot) → bootstrapCITable
  • New visualizations:
    • Agreement heatmap / confusion-matrix plot (agreementHeatmap) with color schemes (blue-red, traffic-light, viridis, grayscale) and count/percentage cell annotations (heatmapColorScheme, heatmapShowCounts, heatmapShowPercentages, heatmapAnnotationSize) → agreementHeatmapPlot
    • Bland-Altman method-comparison output with a Shapiro-Wilk normality check (showBlandAltmanGuide) → blandAltmanHeading, blandAltmanExplanation
    • Rater profile plots — box/violin/bar (raterProfiles, raterProfileType, raterProfileShowPoints) → raterProfilePlot
    • Rater clustering and case clustering with dendrograms and heatmaps — hierarchical/k-means, correlation/euclidean/manhattan/agreement distances, average/complete/single/ward linkage (raterClustering, caseClustering) → raterClusterTable, raterDendrogram, raterClusterHeatmap, caseClusterTable, caseDendrogram, caseClusterHeatmap
    • Stratified agreement-by-subgroup with forest plot (agreementBySubgroup, subgroupVariable, subgroupForestPlot, subgroupMinCases) → subgroupAgreementTable, subgroupForestPlotImage
  • New workflow tools:
    • Paired agreement comparison between two rater conditions with bootstrap (pairedAgreementTest, conditionBVars, pairedBootN) → pairedAgreementTable
    • Sample-size calculator for agreement studies supporting Cohen’s Kappa / Fleiss’ Kappa / ICC (agreementSampleSize, ssMetric, ssKappaNull, ssKappaAlt, ssNRaters, ssNCategories, ssAlpha, ssPower) → agreementSampleSizeTable
  • New computed output variables:
    • Consensus rating variable with majority/supermajority/unanimous rules and tie handling (consensusVar, consensusName, consensusRule, tieBreaker) → consensusTable, consensusVar
    • Case-level Level-of-Agreement categorization — simple/detailed with custom/quartile/tertile thresholds (loaVariable, detailLevel, simpleThreshold, loaThresholds, loaHighThreshold, loaLowThreshold, loaVariableName, showLoaTable) → loaTable, loaDetailTable, loaOutput
  • Other agreement additions:
    • Configurable confidence level for CIs (confLevel)
    • Level-ordering information panel (showLevelInfo) → levelInfoTable
    • Plain-language Summary, About, and Clinical Use Cases panels (showSummary, showAbout) → summary, about, clinicalUseCases
    • New client-side events handler jamovi/js/agreement.events.js (bounds/dependency handling for confLevel, Bland-Altman confidence level, cluster counts, and subgroup minimums)

Enhanced Existing Functions

  • enhancedROC(): Robustness and UX overhaul

    • Rewritten input validation: guards for single-value outcomes, outcome-level checks, and positive-class validation
    • HTML-escaped error/warning messages (private$.safeHtmlOutput) and a notices framework (.addNotice/.renderNotices) plus a methods-explanation panel and instructions
    • Sensible defaults now ON: youdenOptimization, rocCurve, aucTable, optimalCutoffs, diagnosticMetrics; customCutoffs now defaults to empty
    • Added clearWith to results so outputs invalidate correctly; removed dead commented-out time-dependent AUC/ROC stubs

  • psychopdaroc(): Input hardening and cleanup

    • Bootstrap/threshold count options changed from Number to Integer (boot_runs, maxThresholds, bootstrapReps, idiNriBootRuns)
    • Removed dead commented-out option stubs (effectSizeMethod, advancedMetrics); added clearWith to results

  • kappasizeci(): One-sided confidence intervals

    • New citype option (two-sided vs one-sided lower-bound-only), wired to kappaSize::CIBinary/CI3Cats/CI4Cats/CI5Cats, with a UI ComboBox that disables the upper-limit input in one-sided mode
    • New plain-language text_summary output (CI type, lower limit, precision width)

  • kappasizefixedn() / kappasizepower(): New plain-language text_summary output panel

  • nogoldstandard(): New notices panel (“Important Information”) with plain-text notice rendering that resets on each run

  • decisioncalculator(): Sensitivity/specificity confidence intervals now use a logit transformation with continuity correction (sens_se = sqrt(1/TP + 1/FN), spec_se = sqrt(1/TN + 1/FP)) when a zero cell is present — consistent with the existing PPV/NPV CI logic — falling back to exact Clopper-Pearson binomial CIs otherwise

Package Infrastructure

  • Version bumped 0.0.32.69 → 0.0.46; release date 2026-07-04; minimum jamovi app raised to 2.7.27 (minApp)
  • New Imports: ggraph, grDevices, graphics, htmltools, igraph, irrCAC, knitr, stats, tibble, tools (irrCAC/stats/psych back the new chance-corrected, clustering, and ICC agreement measures; ggraph/igraph back the reimplemented decisiongraph tree visualization; htmltools/knitr/tibble/tools/grDevices/graphics support HTML output and plotting)
  • Switched documentation config to Config/roxygen2/version: 8.0.0
  • New shared helper files: R/diagnostichelpers.R (reusable sensitivity/specificity/PPV/NPV helpers) and R/error_handling.R (clinical error-handling framework: clinicopath_init, clinicopath_error_handler)
  • Added .escapeVariableNames and refactored/hardened existing R/utils.R helpers (%notin%/%!in% rewritten as explicit functions, load_required_package default flipped to install_if_missing = FALSE, print.sensSpecTable given an S3-compliant (x, ...) signature)
  • R/decisiongraph_utils.R: decision-tree visualization reimplemented as a real igraph/ggraph dendrogram renderer (graph_from_data_frame, ggraph::geom_edge_diagonal/geom_node_point/geom_node_label, horizontal/vertical/radial layouts) replacing the “Not Yet Implemented” placeholder, plus removal of the hardcoded 0.7/0.2/0.1 Markov transition-matrix stub (decisiongraph is a shipped utility, not a registered menu analysis)

Data

  • Removed five raw CSV files from data/ (cancer_biomarker_data.csv, cardiac_troponin_data.csv, dca_test_data.csv, sepsis_biomarker_data.csv, thyroid_function_data.csv)
  • Added roxygen dataset documentation in R/data.R for the packaged datasets (histopathology, Bayesian DCA, breast cancer, breast/lymphoma diagnostic-styles, thyroid function, and the cancer/cardiac/sepsis/thyroid diagnostic sets plus the combined master collection)

Minor Changes

meddecide 0.0.32.69 (2026-01-02)

New Features

  • bootstrapNRI(): Exported bootstrapNRI function for Net Reclassification Improvement (NRI) bootstrap confidence interval estimation
    • Enables direct access to NRI bootstrap analysis
    • Provides robust confidence intervals for categorical and continuous NRI
    • Supports custom thresholds for risk category definitions
    • Configurable bootstrap iterations and confidence levels

Bug Fixes

  • Fixed critical bug in computeNRI() where risk category labels were incorrectly calculated
    • Corrected the labels vector calculation from 1:length(breaks - 1) to 1:(length(breaks) - 1)
    • This fix ensures proper risk categorization in NRI calculations
    • Affects categorical NRI computations in ROC and psychoPDA analyses
  • agreement(): Fixed stability issues and hanging during initial run
    • Refactored agreement.b.R to ensure responsiveness
    • Maintained support for numeric variables in agreement analysis

Minor Changes

  • Updated package version to 0.0.32.69
  • Synchronized version across DESCRIPTION and jamovi module files (jamovi/0000.yaml)

meddecide 0.0.31.84 (2025-10-03)

Major Changes

New Analysis Functions

  • decisioncombine(): New function for systematic evaluation of diagnostic test combinations
    • Analyzes all possible test result patterns (2-test: 4 patterns, 3-test: 8 patterns)
    • Calculates sensitivity, specificity, PPV, NPV, and accuracy for each pattern combination
    • Identifies optimal testing strategies based on Youden’s J index
    • Includes visualization options: bar charts, heatmaps, forest plots, and decision trees
    • Supports filtering by statistic type and pattern type
    • Can add test pattern column to dataset for further analysis
  • cotest(): New function for analyzing combined results of two concurrent diagnostic tests
    • Calculates post-test probabilities for various scenarios (either positive, both positive, both negative)
    • Supports both parallel and serial testing strategies
    • Provides Fagan nomogram visualizations
  • sequentialtests(): New function for sequential testing analysis
    • Analyzes how diagnostic accuracy changes when applying two tests in sequence
    • Compares three different testing strategies: serial positive (confirmation), serial negative (exclusion), and parallel testing
    • Provides comprehensive analysis including population flow, cost implications, and Fagan nomograms
  • decisioncalculator(): New calculator for diagnostic test evaluation
    • Designed for when you have the four key counts: TP, FP, TN, FN
    • Calculates comprehensive diagnostic performance metrics
    • Supports confidence interval estimation and Fagan nomogram visualization

Enhanced Existing Functions

  • decisioncompare(): Major improvements to test comparison functionality
    • Enhanced comparison plots (bar charts and radar plots)
    • Added statistical comparison using McNemar’s test
    • New summary and explanation options for better interpretation
    • Added manuscript-ready report sentence generation
    • Improved handling of custom prevalence settings
    • Better visualization of confidence intervals for metric differences

Removed Features

  • decisionpanel(): Function removed for future redesign
  • Reorganized jamovi menu structure for better user experience
    • Decision: Core diagnostic test evaluation functions
    • Decision Calculators: Calculator-based tools for specific scenarios
    • ROC: ROC curve analysis functions
    • Agreement: Interrater reliability functions
    • Power Analysis: Sample size calculation functions

Minor Changes

  • Updated agreement() function with improvements to reliability assessment
  • Enhanced documentation across all functions
  • Improved error handling and validation
  • Updated example datasets and usage examples

Bug Fixes

  • Fixed various edge cases in diagnostic metric calculations
  • Improved handling of missing data
  • Enhanced validation of input parameters

meddecide 0.0.31 (2025-09-18)

Package Updates

  • Version synchronization across DESCRIPTION and jamovi module
  • Updated package metadata and author information
  • Enhanced package description with comprehensive feature list

Documentation

  • Improved function documentation with clearer examples
  • Updated pkgdown website structure
  • Added more detailed usage examples for main functions

meddecide 0.0.3.91

New Features

  • Initial implementation of test comparison framework
  • Added support for Fleiss’ Kappa with differentiated method names
  • Enhanced Kappa calculation methods

Bug Fixes

  • Fixed issues with exact Kappa calculations
  • Improved handling of multiple rater scenarios

meddecide 0.0.3.90

Initial Release Features

  • Basic diagnostic test evaluation functions
  • ROC analysis capabilities
  • Interrater reliability assessment (Cohen’s Kappa, Fleiss’ Kappa)
  • Sample size calculations for reliability studies
  • Visualization tools including Fagan nomograms
  • jamovi module integration