Package index • ClinicoPath

All functions

BreastCancer: Wisconsin Breast Cancer Data

ClinicoPath-package ClinicoPath: ClinicoPath: Analysis for Clinicopathological Research

TestROC(): Test ROC

agepyramid(): Age Pyramid

agepyramidClass: Age Pyramid

agreement(): Interrater Reliability

agreementClass: Interrater Reliability Analysis

alluvial(): Alluvial Diagrams

alluvialClass: Alluvial Plot

alluvialSurvival(): Treatment Pathway Alluvial Plot

alluvialSurvivalClass: Alluvial Survival Plot

arcDiagram: Arc Diagram Example Data

auc_ci(): Statistical Utility Functions

bayesdca(): Bayesian Decision Curve Analysis

bayesdcaClass: Bayesian Decision Curve Analysis

bayesdca_test_data: Bayesian Decision Curve Analysis Test Data

benford(): Benford Analysis

benfordClass: Benford's Law Analysis

bootstrapIDI(): Bootstrap IDI calculation with confidence intervals

bootstrapNRI(): Bootstrap NRI calculation with confidence intervals

bootstrap_ci(): Bootstrap confidence intervals for diagnostic metrics

breast_cancer_data: Breast Cancer Screening Data

calculate_auc(): Approximate AUC from sensitivity and specificity

calculate_sensitivity(): Diagnostic metric calculations

calculate_specificity(): Calculate test specificity

cancer_biomarker_data: Cancer Biomarker Data

cardiac_troponin_data: Cardiac Troponin Data for MI Diagnosis

checkdata(): Checking data

chisq.multcomp(): Title

chisqposttest(): Chi-Square Post-Hoc Tests

chisqposttestClass: Chi-Square Post-Hoc Tests

ciSingle(): Confidence interval for a mean

classification(): Decision tree

colon: Colon Cancer Staging and Survival Data

combined_data: Combined Clinical and Event Data

comparingSurvival(): Comparing Survival Outcomes

competingsurvival(): Overall, Cause Specific, and Competing Survival

competingsurvivalClass: Competing Survival Analysis

computeNRI(): Compute Net Reclassification Index (NRI)

consort(): CONSORT Flowchart

consortClass: CONSORT Flowchart

contTables(): Contingency Tables

contTablesPaired(): Paired Samples Contingency Tables

correlation(): Correlation

correlationClass: Correlation Analysis

cotest(): Co-Testing Analysis

cotestClass: Co-Testing Analysis

covid_screening_data: COVID-19 Screening Data

crosstable(): Cross Tables

crosstableClass: Cross Table for Clinicopathological Comparisons

data_longitudinal: Longitudinal Measurement Data

data_percentage: Patient Response Percentage Data

data_raw: Raw Measurement Data Over Time

data_subgroup: Subgroup Analysis Data

date_formats: Date Format Handling Example Data

dca_test: Decision Curve Analysis (DCA) Test Data

dca_test_data: Comprehensive Decision Curve Analysis (DCA) Data

decision(): Medical Decision

decision2(): Decision 2 for using init

decisionClass: Medical Decision Analysis

decisioncalculator(): Medical Decision Calculator

decisioncalculatorClass: Decision Calculator

decisioncombine(): Combine Medical Decision Tests

decisioncombineClass: Combine Medical Decision Tests

decisioncompare(): Compare Medical Decision Tests

decisioncompareClass: Compare Medical Decision Tests

decisioncurve(): Decision Curve Analysis

decisioncurveClass: Decision Curve Analysis

decisionpanel(): Decision Panel Optimization

decisionpanelClass: Decision Panel Optimization

dendogram(): Dendogram

flowchart(): Study Flowchart

flowchartClass: Study Flowchart

groupsummary(): Group and Summarize

groupsummaryClass: Group and Summarize

gtsummary(): Tables via gtsummary

gtsummaryClass: Tables via gtsummary

histopathology: Histopathology Data

hospital_admission_hourly: Hourly Hospital Admission Data

icccoeff(): ICC coefficients

icccoeffClass: Interclass Correlation Coefficient Also see http://www.cookbook-r.com/Statistical_analysis/Inter-rater_reliability/#ordinal-data-weighted-kappa

ihc_test_data: Immunohistochemistry (IHC) Test Data

ihcstats(): IHC Expression Analysis

jjarcdiagram(): Arc Diagram

jjarcdiagramClass: Arc Diagram

jjbarstats(): Bar Charts

jjbarstatsClass: Bar Charts

jjbetweenstats(): Box-Violin Plots to Compare Between Groups

jjbetweenstatsClass: Violin Plots to Compare Between Groups

jjcorrmat(): Correlation Matrix

jjcorrmatClass: Correlation Matrix

jjdotplotstats(): Dot Chart

jjdotplotstatsClass: Dot Chart

jjhistostats(): Histogram

jjhistostatsClass: Histogram

jjpiestats(): Pie Charts

jjpiestatsClass: Pie Charts

jjridgestats(): Ridgeline Plot

jjridgestatsClass: Enhanced Ridgeline Plot

jjscatterstats(): Scatter Plot

jjscatterstatsClass: Scatter Plot

jjstreamgraph(): StreamGraphs

jjstreamgraphClass: StreamGraphs

jjtreemap(): Treemap

jjtreemapClass: Treemap

jjwithinstats(): Box-Violin Plots to Compare Within Groups

jviolin(): Violin Plot

jviolinClass: Violin Plot

kappaSizeCI(): Confidence Interval Approach for the Number of Subjects Required

kappaSizeCIClass: Confidence Interval Approach for the Number of Subjects Required

kappaSizeFixedN(): Lowest Expected Value for a fixed sample size

kappaSizeFixedNClass: Lowest Expected Value for a fixed sample size

kappaSizePower(): Power Approach for the Number of Subjects Required

kappaSizePowerClass: Power Approach for the Number of Subjects Required

lassocox(): Lasso-Cox Regression

lassocoxClass: Lasso-Cox Regression

linechart(): Line Chart

lollipop(): Lollipop Chart

medical_research_data: General Medical Research Data

melanoma: Melanoma Survival Data

mi_ruleout_data: Myocardial Infarction (MI) Rule-Out Data

modelbuilder_test_data: Model Builder Test Data

multisurvival(): Multivariable Survival Analysis

multisurvivalClass: Multivariable Survival Analysis

nogold_standard: No Gold Standard Diagnostic Test Data

nogoldstandard(): Analysis Without Gold Standard

nogoldstandardClass: Analysis Without Gold Standard

nomogram(): Nomogram

nomogrammer(): Fagan Nomogram Function

oddsratio(): Odds Ratio Table and Plot

oddsratioClass: Odds Ratio Table and Plot

oneSurvival(): One Survival Outcome

outcomeorganizer(): Enhanced Outcome Organizer for Survival Analysis

outcomeorganizerClass: Enhanced Outcome Organizer for Survival Analysis

pairchi2(): Pairwise Chi-Square Test

pairchi2Class: Title

parallelplot(): Parallel Plot

patientTimelines: Patient Timeline Data for Clinical Oncology

patientTimelinesDates: Patient Timeline Data with Dates for Clinical Oncology

powersurvival(): Power Analysis for Survival Studies

powersurvivalClass: Power Analysis for Survival Studies

ppv(): Positive Predictive Value

print(<DeLong>): Print Method for DeLong

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

psychopdaroc(): ROC Analysis

psychopdarocClass: ROC Analysis

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

reportcat(): Summary of Categorical Variables

reportcatClass: Summary of Categorical Variables

retracted(): Find Retracted Papers from DOI

retractedClass: Find Retracted Papers from DOI

riverplot(): River Plots

riverplotClass: River Plots

roc(): ROC Curve Analysis

roc2(): ROC

roc2Class: ROC Analysis

rocClass: ROC Curve Analysis

screeningcalculator(): Screening Test Calculator

screeningcalculatorClass: Screening Test Calculator

sequentialtests(): Sequential Testing Analysis

sequentialtestsClass: Sequential Testing Analysis

singlearm(): Single Arm Survival

singlearmClass: Single Arm Survival

stagemigration(): Stage Migration Analysis

stagemigrationClass: Stage Migration Analysis

statsplot2(): Graphs and Plots

statsplot2Class: Plots and Graphs Based on Variable Types

summarydata(): Summary of Continuous Variables

summarydataClass: Summary of Continuous Variables with Distribution Diagnostics

survival(): Survival Analysis

survivalClass: Survival Analysis

survivalcont(): Survival Analysis for Continuous Variable

survivalcontClass: Survival Analysis for Continuous Explanatory Variable

swimmerplot(): Swimmer Plot

swimmerplot2(): Swimmer Plot 2

swimmerplot2Class: Swimmer Plot 2

swimmerplotClass: Swimmer Plot

tableone(): Table One

tableoneClass: Table One

tidyplots(): Tidy Plots

tidyplotsClass: Tidy Plots

timeinterval(): Time Interval Calculator

timeintervalClass: Time Interval Calculator

timeroc(): Time-Dependent ROC Analysis

toolssummary(): Tools for data summary

toolssummaryClass: Tools for data summary

treatmentResponse: Tumor Treatment Response Data

tree(): Medical Decision Tree

treeClass: Medical Decision Tree

tumor_response_examples: Example Tumor Response Datasets

validateROCInputs(): Validate inputs for ROC analysis

vartree(): Variable Tree

vartreeClass: Variable Tree

venn(): Venn Diagram

vennClass: Venn Diagram

vtree3(): Variable Tree V3

vtree3Class: Variable Tree V3

waffle(): Waffle Charts

waffleClass: Waffle Charts

waterfall(): Treatment Response Analysis

waterfallClass: Treatment Response Analysis