NEWS.md

In overdodactyl/diagnosticSummary: Diagnostic Summaries

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

overdodactyl/diagnosticSummary documentation built on Jan. 28, 2024, 10:07 a.m.