Man pages for sbalci/ClinicoPathJamoviModule
Analysis for Clinicopathological Research

agepyramidAge Pyramid
agepyramidClassAge Pyramid
agreementInterrater Reliability
agreementClassInterrater Reliability Analysis
alluvialAlluvial Diagrams
alluvialClassAlluvial Plot
alluvialSurvivalTreatment Pathway Alluvial Plot
alluvialSurvivalClassAlluvial Survival Plot
arcDiagramArc Diagram Example Data
auc_ciStatistical Utility Functions
bayesdcaBayesian Decision Curve Analysis
bayesdcaClassBayesian Decision Curve Analysis
bayesdca_test_dataBayesian Decision Curve Analysis Test Data
benfordBenford Analysis
benfordClassBenford's Law Analysis
bootstrap_ciBootstrap confidence intervals for diagnostic metrics
bootstrapIDIBootstrap IDI calculation with confidence intervals
bootstrapNRIBootstrap NRI calculation with confidence intervals
BreastCancerWisconsin Breast Cancer Data
breast_cancer_dataBreast Cancer Screening Data
calculate_aucApproximate AUC from sensitivity and specificity
calculate_sensitivityDiagnostic metric calculations
calculate_specificityCalculate test specificity
cancer_biomarker_dataCancer Biomarker Data
cardiac_troponin_dataCardiac Troponin Data for MI Diagnosis
checkdataChecking data
chisq.multcompTitle
chisqposttestChi-Square Post-Hoc Tests
chisqposttestClassChi-Square Post-Hoc Tests
ciSingleConfidence interval for a mean
classificationDecision tree
ClinicoPath-packageClinicoPath: Analysis for Clinicopathological Research
colonColon Cancer Staging and Survival Data
combined_dataCombined Clinical and Event Data
comparingSurvivalComparing Survival Outcomes
competingsurvivalOverall, Cause Specific, and Competing Survival
competingsurvivalClassCompeting Survival Analysis
computeNRICompute Net Reclassification Index (NRI)
consortCONSORT Flowchart
consortClassCONSORT Flowchart
contTablesContingency Tables
contTablesPairedPaired Samples Contingency Tables
correlationCorrelation
correlationClassCorrelation Analysis
cotestCo-Testing Analysis
cotestClassCo-Testing Analysis
covid_screening_dataCOVID-19 Screening Data
crosstableCross Tables
crosstableClassCross Table for Clinicopathological Comparisons
data_longitudinalLongitudinal Measurement Data
data_percentagePatient Response Percentage Data
data_rawRaw Measurement Data Over Time
data_subgroupSubgroup Analysis Data
date_formatsDate Format Handling Example Data
dca_testDecision Curve Analysis (DCA) Test Data
dca_test_dataComprehensive Decision Curve Analysis (DCA) Data
decisionMedical Decision
decision2Decision 2 for using init
decisioncalculatorMedical Decision Calculator
decisioncalculatorClassDecision Calculator
decisionClassMedical Decision Analysis
decisioncombineCombine Medical Decision Tests
decisioncombineClassCombine Medical Decision Tests
decisioncompareCompare Medical Decision Tests
decisioncompareClassCompare Medical Decision Tests
decisioncurveDecision Curve Analysis
decisioncurveClassDecision Curve Analysis
decisionpanelDecision Panel Optimization
decisionpanelClassDecision Panel Optimization
dendogramDendogram
flowchartStudy Flowchart
flowchartClassStudy Flowchart
groupsummaryGroup and Summarize
groupsummaryClassGroup and Summarize
gtsummaryTables via gtsummary
gtsummaryClassTables via gtsummary
histopathologyHistopathology Data
hospital_admission_hourlyHourly Hospital Admission Data
icccoeffICC coefficients
icccoeffClassInterclass Correlation Coefficient Also see...
ihcstatsIHC Expression Analysis
ihc_test_dataImmunohistochemistry (IHC) Test Data
jjarcdiagramArc Diagram
jjarcdiagramClassArc Diagram
jjbarstatsBar Charts
jjbarstatsClassBar Charts
jjbetweenstatsBox-Violin Plots to Compare Between Groups
jjbetweenstatsClassViolin Plots to Compare Between Groups
jjcorrmatCorrelation Matrix
jjcorrmatClassCorrelation Matrix
jjdotplotstatsDot Chart
jjdotplotstatsClassDot Chart
jjhistostatsHistogram
jjhistostatsClassHistogram
jjpiestatsPie Charts
jjpiestatsClassPie Charts
jjridgestatsRidgeline Plot
jjridgestatsClassEnhanced Ridgeline Plot
jjscatterstatsScatter Plot
jjscatterstatsClassScatter Plot
jjstreamgraphStreamGraphs
jjstreamgraphClassStreamGraphs
jjtreemapTreemap
jjtreemapClassTreemap
jjwithinstatsBox-Violin Plots to Compare Within Groups
jviolinViolin Plot
jviolinClassViolin Plot
kappaSizeCIConfidence Interval Approach for the Number of Subjects...
kappaSizeCIClassConfidence Interval Approach for the Number of Subjects...
kappaSizeFixedNLowest Expected Value for a fixed sample size
kappaSizeFixedNClassLowest Expected Value for a fixed sample size
kappaSizePowerPower Approach for the Number of Subjects Required
kappaSizePowerClassPower Approach for the Number of Subjects Required
lassocoxLasso-Cox Regression
lassocoxClassLasso-Cox Regression
linechartLine Chart
lollipopLollipop Chart
medical_research_dataGeneral Medical Research Data
melanomaMelanoma Survival Data
mi_ruleout_dataMyocardial Infarction (MI) Rule-Out Data
modelbuilder_test_dataModel Builder Test Data
multisurvivalMultivariable Survival Analysis
multisurvivalClassMultivariable Survival Analysis
nogoldstandardAnalysis Without Gold Standard
nogold_standardNo Gold Standard Diagnostic Test Data
nogoldstandardClassAnalysis Without Gold Standard
nomogramNomogram
nomogrammerFagan Nomogram Function
oddsratioOdds Ratio Table and Plot
oddsratioClassOdds Ratio Table and Plot
oneSurvivalOne Survival Outcome
outcomeorganizerEnhanced Outcome Organizer for Survival Analysis
outcomeorganizerClassEnhanced Outcome Organizer for Survival Analysis
pairchi2Pairwise Chi-Square Test
pairchi2ClassTitle
parallelplotParallel Plot
patientTimelinesPatient Timeline Data for Clinical Oncology
patientTimelinesDatesPatient Timeline Data with Dates for Clinical Oncology
pipePipe operator from...
powersurvivalPower Analysis for Survival Studies
powersurvivalClassPower Analysis for Survival Studies
ppvPositive Predictive Value
print.DeLongPrint Method for DeLong
print.sensSpecTablePrint formatted HTML table for sensitivity/specificity...
psychopdarocROC Analysis
psychopdarocClassROC Analysis
raw_to_probConvert raw test values to predicted probabilities using ROC...
reportcatSummary of Categorical Variables
reportcatClassSummary of Categorical Variables
retractedFind Retracted Papers from DOI
retractedClassFind Retracted Papers from DOI
riverplotRiver Plots
riverplotClassRiver Plots
rocROC Curve Analysis
roc2ROC
roc2ClassROC Analysis
rocClassROC Curve Analysis
screeningcalculatorScreening Test Calculator
screeningcalculatorClassScreening Test Calculator
sequentialtestsSequential Testing Analysis
sequentialtestsClassSequential Testing Analysis
singlearmSingle Arm Survival
singlearmClassSingle Arm Survival
stagemigrationStage Migration Analysis
stagemigrationClassStage Migration Analysis
statsplot2Graphs and Plots
statsplot2ClassPlots and Graphs Based on Variable Types
summarydataSummary of Continuous Variables
summarydataClassSummary of Continuous Variables with Distribution Diagnostics
survivalSurvival Analysis
survivalClassSurvival Analysis
survivalcontSurvival Analysis for Continuous Variable
survivalcontClassSurvival Analysis for Continuous Explanatory Variable
swimmerplotSwimmer Plot
swimmerplot2Swimmer Plot 2
swimmerplot2ClassSwimmer Plot 2
swimmerplotClassSwimmer Plot
tableoneTable One
tableoneClassTable One
TestROCTest ROC
tidyplotsTidy Plots
tidyplotsClassTidy Plots
timeintervalTime Interval Calculator
timeintervalClassTime Interval Calculator
timerocTime-Dependent ROC Analysis
toolssummaryTools for data summary
toolssummaryClassTools for data summary
treatmentResponseTumor Treatment Response Data
treeMedical Decision Tree
treeClassMedical Decision Tree
tumor_response_examplesExample Tumor Response Datasets
validateROCInputsValidate inputs for ROC analysis
vartreeVariable Tree
vartreeClassVariable Tree
vennVenn Diagram
vennClassVenn Diagram
vtree3Variable Tree V3
vtree3ClassVariable Tree V3
waffleWaffle Charts
waffleClassWaffle Charts
waterfallTreatment Response Analysis
waterfallClassTreatment Response Analysis
sbalci/ClinicoPathJamoviModule documentation built on June 13, 2025, 9:34 a.m.