sbalci/ClinicoPathJamoviModule

---
title: Common Analysis for Clinicopathological Research
name: ClinicoPath
version: 0.0.2.26
jms: '1.0'
authors:
  - Serdar Balci
maintainer: Serdar Balci <drserdarbalci@gmail.com>
date: '2024-01-19'
type: R
description: >-
  ClinicoPath help researchers to generate natural language summaries of their
  dataset, generate cross tables with statistical tests, and survival analysis
  with survival tables, survival plots, and natural language summaries.
analyses:
  - title: Age Pyramid
    name: agepyramid
    ns: ClinicoPath
    menuGroup: Exploration
    menuTitle: Age Pyramid
    menuSubgroup: ClinicoPath Descriptive Plots
  - title: Alluvial Diagrams
    name: alluvial
    ns: ClinicoPath
    menuGroup: Exploration
    menuSubgroup: ClinicoPath Descriptive Plots
    menuTitle: Alluvial Diagrams
  - title: Benford Analysis
    name: benford
    ns: ClinicoPath
    menuGroup: Exploration
    menuSubgroup: ClinicoPath Descriptives
    menuTitle: Benford Analysis
  - title: Cross Tables
    name: crosstable
    ns: ClinicoPath
    menuGroup: Exploration
    menuSubgroup: ClinicoPath Comparisons
    menuTitle: Cross Tables
    description: Function for making Cross Tables.
  - title: Summary of Categorical Variables
    name: reportcat
    ns: ClinicoPath
    menuGroup: Exploration
    menuSubgroup: ClinicoPath Descriptives
    menuTitle: Summary of Categorical Variables
    description: Function for Generating Summaries for Categorical Variables.
  - title: Summary of Continuous Variables
    name: summarydata
    ns: ClinicoPath
    menuGroup: Exploration
    menuSubgroup: ClinicoPath Descriptives
    menuTitle: Summary of Continuous Variables
    description: Function for Generating Summaries for Continuous Variables.
  - title: Table One
    name: tableone
    ns: ClinicoPath
    menuGroup: Exploration
    menuSubgroup: ClinicoPath Descriptives
    menuTitle: Table One
    description: Function for making Table One.
  - title: Variable Tree
    name: vartree
    ns: ClinicoPath
    menuGroup: Exploration
    menuSubgroup: ClinicoPath Descriptive Plots
    menuTitle: Variable Tree
    description: Function for Generating Tree Summaries of Variables.
  - title: Venn Diagram
    name: venn
    ns: ClinicoPath
    menuGroup: Exploration
    menuSubgroup: ClinicoPath Descriptive Plots
    menuTitle: Venn Diagram
  - title: Survival Analysis
    name: survival
    ns: ClinicoPath
    menuGroup: Survival
    menuSubgroup: ClinicoPath Survival
    menuTitle: Survival Analysis
    menuSubtitle: 'Univariate Survival Analysis, Cox, Kaplan-Meier, 1,3,5-yr'
    description: Function for Generating Summaries for Survival Analysis.
  - title: Survival Analysis for Continuous Variable
    name: survivalcont
    ns: ClinicoPath
    menuGroup: Survival
    menuSubgroup: ClinicoPath Survival
    menuTitle: Survival Analysis for Continuous Variable
    menuSubtitle: Cut-off & Univariate Survival Analysis
  - title: Multivariable Survival Analysis
    name: multisurvival
    ns: ClinicoPath
    menuGroup: Survival
    menuSubgroup: ClinicoPath Survival
    menuTitle: Multivariable Survival Analysis
    menuSubtitle: 'Multivariable Cox-regression, Adjusted Survival'
    description: Function for Multivariable Survival Analysis using Cox-regression.
  - title: Odds Ratio Table and Plot
    name: oddsratio
    ns: ClinicoPath
    menuGroup: Survival
    menuSubgroup: ClinicoPath Survival
    menuTitle: Odds Ratio Table and Plot
    menuSubtitle: Odds Ratio for Binary Outcomes
    description: Function for Odds Ratio Table and Plot.
  - title: Interrater Reliability
    name: agreement
    ns: ClinicoPath
    menuGroup: meddecide
    menuSubgroup: Agreement
    menuTitle: Interrater Reliability
    description: Function for Interrater Reliability.
  - title: Medical Decision
    name: decision
    ns: ClinicoPath
    menuGroup: meddecide
    menuSubgroup: Decision
    menuTitle: Medical Decision
    menuSubtitle: 'Sensitivity, Specificity, PPV, NPV, ...'
    description: >
      Function for Medical Decision Analysis. Sensitivity, specificity, positive
      predictive value, negative predictive value.
  - title: Medical Decision Calculator
    name: decisioncalculator
    ns: ClinicoPath
    menuGroup: meddecide
    menuSubgroup: Decision
    menuTitle: Medical Decision Calculator
    menuSubtitle: 'Sensitivity, Specificity, PPV, NPV, ...'
    description: Function for Medical Decision Calculator.
  - title: Decision Tree
    name: tree
    ns: ClinicoPath
    menuGroup: meddecide
    menuSubgroup: Drafts
    menuTitle: Decision Tree
    description: Function for making Decision Trees.
    menuSubtitle: Classification
  - title: Find Retracted Papers from DOI
    name: retracted
    ns: ClinicoPath
    menuGroup: Exploration
    menuSubgroup: Drafts
    menuTitle: Find Retracted Papers from DOI
    menuSubtitle: Bibliometrics
  - title: Box-Violin Plots to Compare Within Groups
    name: jjwithinstats
    ns: ClinicoPath
    menuGroup: JJStatsPlot
    menuSubgroup: Categorical vs Continuous
    menuTitle: Box-Violin Plots to Compare Within Groups
    menuSubtitle: Repeated Continuous Measurements
  - title: Histogram
    name: jjhistostats
    ns: ClinicoPath
    menuGroup: JJStatsPlot
    menuSubgroup: Continuous
    menuTitle: Histogram
    description: |
      'Wrapper Function for ggstatsplot::gghistostats and
      ggstatsplot::grouped_gghistostats to generate Histogram.'
  - title: Checking data
    name: checkdata
    ns: ClinicoPath
    menuGroup: fromOthers
    menuTitle: Checking data
    menuSubgroup: PUBH5018
  - title: Confidence interval for a mean
    name: ciSingle
    ns: ClinicoPath
    menuGroup: fromOthers
    menuTitle: Confidence interval for a mean
    menuSubgroup: PUBH5018
  - title: Decision tree
    name: classification
    ns: ClinicoPath
    menuGroup: meddecide
    menuTitle: Decision tree
    menuSubgroup: Drafts
    menuSubtitle: Classification
  - title: Comparing Survival Outcomes
    name: comparingSurvival
    ns: ClinicoPath
    menuGroup: Survival
    menuTitle: Comparing Survival Outcomes
    menuSubgroup: Drafts
    menuSubtitle: SimpleSurvival
  - title: 'Overall, Cause Specific, and Competing Survival'
    name: competingsurvival
    ns: ClinicoPath
    menuGroup: Survival
    menuSubgroup: Drafts
    menuTitle: 'Overall, Cause Specific, and Competing Survival'
    menuSubtitle: Survival for Different Outcomes
    description: 'Overall, Cause Specific, and Competing Survival.'
  - title: Contingency Tables
    name: contTables
    ns: ClinicoPath
    menuGroup: fromOthers
    menuSubgroup: Frequencies Contingency Tables
    menuTitle: Independent Samples
    menuSubtitle: χ² test of association
    description: >
      The χ² test of association (not to be confused with the χ² goodness of
      fit) is used to test whether two categorical variables are independent or
      associated. If the p-value is low, it suggests the variables are not
      independent, and that there is a relationship between the two variables.
  - title: Paired Samples Contingency Tables
    name: contTablesPaired
    ns: ClinicoPath
    menuGroup: fromOthers
    menuSubgroup: Frequencies Contingency Tables
    menuTitle: Paired Samples
    menuSubtitle: McNemar test
    description: McNemar test
  - title: Correlation
    name: correlation
    ns: ClinicoPath
    menuGroup: Exploration
    menuSubgroup: Drafts
    menuTitle: Correlation
    description: Function for Correlation.
    menuSubtitle: Correlation
  - title: Decision 2 for using init
    name: decision2
    ns: ClinicoPath
    menuGroup: meddecide
    menuSubgroup: Drafts
    menuTitle: Decision 2 for using init
    menuSubtitle: 'Sensitivity, Specificity, PPV, NPV, ...'
    description: >
      Function for Medical Decision Analysis. Sensitivity, specificity, positive
      predictive value, negative predictive value.
  - title: Dendogram
    name: dendogram
    ns: ClinicoPath
    menuGroup: meddecide
    menuTitle: Dendogram
    menuSubgroup: Drafts
  - title: Tables via gtsummary
    name: gtsummary
    ns: ClinicoPath
    menuGroup: Exploration
    menuSubgroup: Drafts
    menuTitle: Tables via gtsummary
    menuSubtitle: Comparisons
  - title: ICC coefficients
    name: icccoeff
    ns: ClinicoPath
    menuGroup: meddecide
    menuSubgroup: Drafts
    menuTitle: ICC coefficients
    description: Function for Interclass Correlation Coefficient Calculation.
    menuSubtitle: Agreement
  - title: Graphs and Plots
    name: statsplot2
    ns: ClinicoPath
    menuGroup: Graphs
    menuSubgroup: Drafts JJStatsPlot
    menuTitle: Graphs and Plots
    description: Function for Generating Plots and Graphs Based on Variable Types.
    menuSubtitle: Variable Type Based Graphs and Plots
  - title: Bar Charts
    name: jjbarstats
    ns: ClinicoPath
    menuGroup: JJStatsPlot
    menuSubgroup: Categorical vs Categorical
    menuTitle: Bar Charts
    description: |
      'Wrapper Function for ggstatsplot::ggbarstats and
      ggstatsplot::grouped_ggbarstats to generate Bar Charts.'
  - title: Box-Violin Plots to Compare Between Groups
    name: jjbetweenstats
    ns: ClinicoPath
    menuGroup: JJStatsPlot
    menuSubgroup: Categorical vs Continuous
    menuTitle: Box-Violin Plots to Compare Between Groups
    menuSubtitle: Independent Samples
  - title: Correlation Matrix
    name: jjcorrmat
    ns: ClinicoPath
    menuGroup: JJStatsPlot
    menuSubgroup: Continuous vs Continuous
    menuTitle: Correlation Matrix
  - title: Dot Chart
    name: jjdotplotstats
    ns: ClinicoPath
    menuGroup: JJStatsPlot
    menuSubgroup: Categorical vs Continuous
    menuTitle: Dot Chart
  - title: Pie Charts
    name: jjpiestats
    ns: ClinicoPath
    menuGroup: JJStatsPlot
    menuSubgroup: Categorical vs Categorical
    menuTitle: Pie Charts
  - title: Scatter Plot
    name: jjscatterstats
    ns: ClinicoPath
    menuGroup: JJStatsPlot
    menuSubgroup: Continuous vs Continuous
    menuTitle: Scatter Plot
  - title: Violin Plot
    name: jviolin
    ns: ClinicoPath
    menuGroup: Graphs
    menuSubgroup: Drafts
    menuTitle: Violin Plot
    menuSubtitle: R Graph Gallery Violin
  - title: Line Chart
    name: linechart
    ns: ClinicoPath
    menuGroup: Graphs
    menuSubgroup: Drafts
    menuTitle: Line Chart
    menuSubtitle: Exploration
  - title: Lollipop Chart
    name: lollipop
    ns: ClinicoPath
    menuGroup: Graphs
    menuSubgroup: Drafts
    menuTitle: Lollipop Chart
  - title: Nomogram
    name: nomogram
    ns: ClinicoPath
    menuGroup: meddecide
    menuTitle: Nomogram
    menuSubgroup: Drafts
  - title: One Survival Outcome
    name: oneSurvival
    ns: ClinicoPath
    menuGroup: Survival
    menuTitle: One Survival Outcome
    menuSubgroup: Drafts
    menuSubtitle: SimpleSurvival
  - title: Pairwise Chi-Square Test
    name: pairchi2
    ns: ClinicoPath
    menuGroup: Exploration
    menuTitle: Pairwise Chi-Square Test
    menuSubgroup: Drafts
    menuSubtitle: Association
  - title: Parallel Plot
    name: parallelplot
    ns: ClinicoPath
    menuGroup: Graphs
    menuTitle: Parallel Plot
    menuSubgroup: Drafts
    menuSubtitle: Exploration
  - title: Positive Predictive Value
    name: ppv
    ns: ClinicoPath
    menuGroup: meddecide
    menuTitle: Positive Predictive Value
    menuSubgroup: Drafts
  - title: ROC
    name: roc
    ns: ClinicoPath
    menuGroup: meddecide
    menuSubgroup: Drafts
    menuTitle: ROC
    description: Function for ROC Analysis.
    menuSubtitle: Decision
  - title: Time Interval
    name: timeinterval
    ns: ClinicoPath
    menuGroup: Survival
    menuSubgroup: Drafts
    menuTitle: Time Interval
    menuSubtitle: Time Interval
  - title: Tools for data summary
    name: toolssummary
    ns: ClinicoPath
    menuGroup: Exploration
    menuTitle: Tools for data summary
    menuSubgroup: Drafts
  - title: Confidence Interval Approach for the Number of Subjects Required
    name: kappaSizeCI
    ns: ClinicoPath
    menuGroup: meddecide
    menuSubgroup: Power Analysis
    menuTitle: Confidence Interval Approach for the Number of Subjects Required
    menuSubtitle: Find sample size based on Kappa confidence
    description: |
      Power Analysis for Interobserver Agreement Analysis.
  - title: Lowest Expected Value for a fixed sample size
    name: kappaSizeFixedN
    ns: ClinicoPath
    menuGroup: meddecide
    menuSubgroup: Power Analysis
    menuTitle: Lowest Expected Value for a fixed sample size
    menuSubtitle: Find lower Kappa based on sample size
    description: |
      Lowest Expected Value for a fixed sample size.
  - title: Power Approach for the Number of Subjects Required
    name: kappaSizePower
    ns: ClinicoPath
    menuGroup: meddecide
    menuSubgroup: Power Analysis
    menuTitle: Power Approach for the Number of Subjects Required
    menuSubtitle: Find sample size based on power
    description: |
      Power Analysis for Interobserver Agreement Analysis.
  - title: Single Arm Survival
    name: singlearm
    ns: ClinicoPath
    menuGroup: Survival
    menuSubgroup: ClinicoPath Survival
    menuTitle: Single Arm Survival
    menuSubtitle: 'Survival for whole group, no explanatory factor'
    description: Function for Generating Summaries for Survival Analysis.
  - title: Test ROC
    name: TestROC
    ns: ClinicoPath
    menuGroup: fromOthers
    menuTitle: Test ROC
    menuSubgroup: PPDA
datasets:
  - name: histopathology including analysis
    path: histopathologyDescriptives.omv
    description: Example analysis for descriptive functions.
    tags:
      - Table One
      - Data Summary
      - Cross Tables
      - Alluvial Diagrams
  - name: histopathology including analysis
    path: histopathologySurvival.omv
    description: Example survival analysis for histopathology data
    tags:
      - Survival
      - Natural Language
  - name: histopathology including analysis
    path: histopathologyMedicalDecision.omv
    description: Example analysis for Medical Decision Tests.
    tags:
      - Kappa
      - Sensitivity
  - name: histopathology including analysis
    path: histopathologyGraphsPlots.omv
    description: Examples for Graphs and Plots
    tags:
      - GGStatsPlot
      - Histogram
      - Violin Plots
      - Bar Charts
      - Pie Charts
      - Dot Charts
      - Scatter Plots
      - Correlation Matrix
  - name: histopathology data only
    path: histopathology.omv
    description: Fake histopathology research data for ClinicoPath module
    tags:
      - Table One
      - Data Summary
      - Survival
  - name: melanoma
    path: melanoma.omv
    description: 'melanoma dataset obtained from {boot}.'
    tags:
      - Data Summary
      - Survival
      - Competing risks regression
  - name: colon
    path: colon.omv
    description: 'colon cancer dataset, obtained from {survival}.'
    tags:
      - Data Summary
      - Survival
  - name: BreastCancer
    path: BreastCancer.omv
    description: 'Wisconsin Breast Cancer Database dataset, obtained from {mlbench}.'
    tags:
      - Classification
  - name: rocdata
    path: rocdata.omv
    description: Example data for ROC analysis.
    tags:
      - ROC
usesNative: true
minApp: 1.8.0

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