Man pages for sbalci/ClinicoPathJamoviModule
Analysis for Clinicopathological Research
| 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 |
| bootstrap_ci | Bootstrap confidence intervals for diagnostic metrics |
| bootstrapIDI | Bootstrap IDI calculation with confidence intervals |
| bootstrapNRI | Bootstrap NRI calculation with confidence intervals |
| BreastCancer | Wisconsin Breast Cancer Data |
| 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 |
| ClinicoPath-package | ClinicoPath: Analysis for Clinicopathological Research |
| 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 |
| decisioncalculator | Medical Decision Calculator |
| decisioncalculatorClass | Decision Calculator |
| decisionClass | Medical Decision Analysis |
| 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... |
| ihcstats | IHC Expression Analysis |
| ihc_test_data | Immunohistochemistry (IHC) Test Data |
| 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... |
| kappaSizeCIClass | Confidence Interval Approach for the Number of Subjects... |
| 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 |
| nogoldstandard | Analysis Without Gold Standard |
| nogold_standard | No Gold Standard Diagnostic Test Data |
| 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 |
| pipe | Pipe operator from... |
| 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... |
| psychopdaroc | ROC Analysis |
| psychopdarocClass | ROC Analysis |
| raw_to_prob | Convert raw test values to predicted probabilities using ROC... |
| 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 |
| TestROC | Test ROC |
| 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 |
