Package index • OncoPath

Main Analysis Functions

Core functions for oncological and pathological research

swimmerplot(): Swimmer Plot

swimmerplotClass: Swimmer Plot

waterfall(): Treatment Response Analysis

waterfallClass: Treatment Response Analysis

diagnosticmeta(): Diagnostic Test Meta-Analysis for Pathology

diagnosticmetaClass: Diagnostic Test Meta-Analysis for Pathology

ihcheterogeneity(): IHC Heterogeneity Analysis

Diagnostic Test Functions

Functions for diagnostic test accuracy analysis

calculate_sensitivity(): Calculate test sensitivity

calculate_specificity(): Calculate test specificity

calculate_ppv(): Calculate positive predictive value (PPV)

calculate_npv(): Calculate negative predictive value (NPV)

calculate_plr(): Calculate positive likelihood ratio

calculate_nlr(): Calculate negative likelihood ratio

calculate_auc(): Approximate AUC from sensitivity and specificity

validateROCInputs(): Validate inputs for ROC analysis

bootstrapIDI(): Bootstrap IDI calculation with confidence intervals

IHC Analysis Functions

Immunohistochemistry marker analysis utilities

validateIHCData(): Validate IHC Data Requirements

validateIHCClustering(): Validate IHC Clustering Parameters

convertIHCToNumeric(): Convert IHC Marker Data to Numeric Matrix

convertIHCMarkerToNumeric(): Convert IHC Marker Data Types Safely

calculateIHCMarkerSummary(): Calculate IHC Marker Summary Statistics

calculateHScore(): Calculate H-Score from Intensity and Proportion

calculateIHCDistance(): Calculate Distance Matrix for IHC Data

calculateIHCSilhouette(): Calculate Silhouette Analysis for Clustering Quality

showIHCDataRequirements(): Generate IHC Data Requirements HTML

IHC Visualization Functions

Functions for IHC visualization and theming

getIHCTheme(): Get Professional IHC Visualization Theme

getIHCColorPalette(): Get Professional Color Palette for IHC Visualizations

formatIHCPValue(): Format P-values Consistently for IHC Reports

getIHCSignificanceStars(): Get Significance Stars for P-values

Utility Functions

Helper functions for data processing

safe_divide(): Safe division function

prop_to_percent(): Convert proportion to percentage string

raw_to_prob(): Convert raw test values to predicted probabilities using ROC curve

is_in_range(): Check if value is within valid range

load_required_package(): Load required packages with error handling

`%>%`: Pipe operator

Print Methods

Custom print methods

print(<sensSpecTable>): Print formatted HTML table for sensitivity/specificity results

Package Information

Package startup and information

clinicopath_startup_message(): Package startup message

hello(): Hello, World!