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Changelog

Source: NEWS.md

diagnosticSummary 0.0.2.00

New metrics

  • Prevalence
  • False Negative Rate
  • False Positive Rate
  • False Discovery Rate
  • PR AUC
  • Cohen’s Kappa
  • Matthews Correlation Coefficient
  • Balanced Accuracy
  • F-beta
  • F2
  • Informedness
  • Markedness
  • G-mean
  • Fowlkes-Mallows Index
  • Brier Score
  • Detection Prevalence
  • No Information Rate (NIR)

Also added aliases for metrics with the same name (e.g., recall and true positive rate for sensitivity)

New/modified tests

  • Breslow and Day test implemented within package
  • Added Chi-Square Test
  • Added Fisher’s Exact Test
  • Added G-Test (Log-Likelihood Ratio Test)
  • Added McNemar’s Chi-squared Test for Paired Proportions
  • Added Z-test for Comparing Two Proportions
  • Added DeLong’s Test for Comparing Two ROC Curves

New output

  • Added thresholds to the output of dx containing metrics across a full range of thresholds
  • Added prevalence to the output of dx containing metrics across a full range of prevalencies
  • Added rank to the output of dx containing rank-based summaries from predicted probabilities

Changes to dx_obj$measures output

  • rawestime column renamed to estimate
  • rawuci and rawlci column renamed to conf_low and conf_high

New plots

  • Added lift curve: dx_plot_lift
  • Added Kolmogorov-Smirnov plot: dx_plot_ks
  • Added cumulative gains chart: dx_plot_gain
  • Added Precision-Recall plot: dx_plot_pr
  • Added NPV and PPV across prevalencies: dx_plot_predictive_value
  • Added calibration curve: dx_plot_calibration
  • Added decision curve: dx_plot_decision_curve
  • Added Youden’s J Index Curve: dx_plot_youden_j
  • Added Cumulative Accuracy Profile (CAP) curve: dx_plot_cap
  • Added cost curve: dx_plot_cost
  • Added plot showing metrics across thresholds: dx_plot_thresholds
  • Add ability to plot multiple ROC curves: dx_plot_rocs

Renamed Functions

  • The confusion matrix plot was renamed from dx_cm to dx_plot_cm (dx_cm now constructs the confusion matrix)
  • dx_roc was renamed dx_plot_roc
  • dx_forest was renamed dx_plot_forest

Bug Fixes

  • Breslow-Day test no longer silently left out if DescTools not installed
  • levels argument in as.data.frame and summary didn’t filter to label column

Dependencies

  • Removed dplyr, scales, boot, and tidyr from Imports
  • Moved gtable, grid, and gridExtra to Suggests
  • Removed DescTools and e1071 from Suggests
  • Added tibble to Suggests

Comparison of dx objects

  • New dx_compare function to run pairwise tests on a list of dx_objects

Documentation

  • Added a NEWS.md file to track changes to the package.
  • Added documentation/descriptions/details to all functions
  • Migrated pkgdown website to bootstrap 5