WIP demo app with all modules

README_clinical_modules_demo.md

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+# Complete Teal Clinical Modules Demo App
+
+This Shiny application demonstrates **ALL 37 available modules** from the `teal.modules.clinical` package in a comprehensive, organized interface.
+
+## Overview
+
+The app showcases the complete range of clinical trial analysis modules available in the `teal.modules.clinical` package, providing a comprehensive example of how to integrate all these modules into a single application.
+
+## Features
+
+### 1. **App Information**
+- Front page with detailed information about the demo
+- Overview of all 37 available modules and data sources
+- Package dependencies and descriptions
+
+### 2. **Data Exploration**
+- **Data Table**: Interactive table viewer for all datasets
+- **Variable Browser**: Explore variables across all datasets
+
+### 3. **Demographics**
+- **Demographic Summary**: Standard demographic table with summary statistics by treatment arm
+
+### 4. **Adverse Events**
+- **AE Summary**: Summary of adverse events with analysis flags
+- **AE by Term**: Adverse events by preferred term and body system
+- **AE Table by Grade**: Adverse events stratified by toxicity grade
+- **AE Rates Adjusted for Patient-Years**: Time-to-event analysis of adverse events
+- **Adverse Events by SMQ Table**: Standardized MedDRA Queries analysis
+
+### 5. **Laboratory Data**
+- **Labs Summary**: Summary statistics for laboratory parameters
+- **Grade Laboratory Abnormality Table**: Laboratory shifts by toxicity grade
+- **Laboratory test results with highest grade post-baseline**: Worst post-baseline laboratory abnormalities
+
+### 6. **Exposure**
+- **Exposure Summary**: Summary of treatment exposure
+- **Duration of Exposure Table**: Detailed exposure duration analysis
+
+### 7. **Vital Signs**
+- **Vital Signs Abnormality**: Analysis of vital signs abnormalities
+
+### 8. **Concomitant Medications**
+- **Concomitant Medication**: Analysis of concomitant medications by ATC classification
+
+### 9. **ECG Data**
+- **ECG Shift Table by Arm**: ECG parameter shifts from baseline
+- **ECG Shift by Arm by Worst Grade**: ECG shifts by arm by worst grade
+
+### 10. **Patient Profiles**
+- **Patient Profile - Basic Info**: Basic patient information tables
+- **Patient Profile - Laboratory**: Laboratory data for individual patients
+- **Patient Profile - Medical History**: Medical history for individual patients
+- **Patient Profile - Prior Medication**: Prior medication data for individual patients
+
+### 11. **Statistical Analysis**
+- **Analysis of Covariance (ANCOVA)**: ANCOVA analysis for laboratory data
+- **Binary Outcome Analysis**: Analysis of binary response variables
+- **Cox Regression Analysis**: Survival analysis using Cox regression
+- **Logistic Regression Analysis**: Logistic regression for binary outcomes
+- **Generalized Linear Models for Counts**: GLM analysis for count data
+- **Time-to-Event Analysis**: General time-to-event analysis
+- **Generalized Estimating Equations (GEE)**: GEE analysis for repeated measures
+- **Mixed Models for Repeated Measures (MMRM)**: MMRM analysis for longitudinal data
+
+### 12. **Graphics**
+- **Laboratory Values Over Time**: Line plots of laboratory values over time
+- **Kaplan-Meier Plot**: Survival analysis plots for time-to-event data
+- **Simple Bar Chart**: Bar charts for laboratory data
+- **Confidence Interval Plot**: CI plots for laboratory data
+- **Forest Plot for Response**: Forest plots for response data
+- **Forest Plot for Time-to-Event**: Forest plots for survival data
+- **Individual Patient Plots**: Individual patient plots for laboratory data
+- **Patient Profile - Adverse Events Plots**: AE plots for individual patients
+- **Patient Profile - Timeline Plots**: Timeline plots for individual patients
+- **Patient Profile - Therapy Plots**: Therapy plots for individual patients
+- **Patient Profile - Vital Signs Plots**: Vital signs plots for individual patients
+
+## Data
+
+The app uses simulated CDISC ADaM datasets generated by the `random.cdisc.data` package:
+
+- **ADSL**: Subject-level data
+- **ADAE**: Adverse events data
+- **ADAETTE**: Time-to-event adverse events data
+- **ADEX**: Exposure data
+- **ADLB**: Laboratory data
+- **ADEG**: ECG data
+- **ADVS**: Vital signs data
+- **ADCM**: Concomitant medications data
+- **ADMH**: Medical history data
+- **ADPM**: Prior medication data
+- **ADRS**: Response data
+- **ADEF**: Efficacy data
+
+## How to Run
+
+1. **Install Required Packages**:
+   ```r
+   install.packages(c("teal", "teal.modules.general", "teal.modules.clinical", "random.cdisc.data"))
+   ```
+
+2. **Run the App**:
+   ```r
+   source("teal_clinical_modules_demo.R")
+   ```
+
+3. **Alternative: Run with Shiny**:
+   ```r
+   library(shiny)
+   source("teal_clinical_modules_demo.R")
+   runApp()
+   ```
+
+## Complete Module List (37 modules)
+
+### **Table Modules (tm_t_*) - 25 modules:**
+1. `tm_t_summary` - Demographic and general summary tables
+2. `tm_t_events_summary` - Adverse events summary
+3. `tm_t_events` - Adverse events by term
+4. `tm_t_events_by_grade` - Adverse events by toxicity grade
+5. `tm_t_events_patyear` - Time-to-event analysis
+6. `tm_t_smq` - Standardized MedDRA Queries
+7. `tm_t_summary_by` - Summary tables with grouping
+8. `tm_t_shift_by_grade` - Laboratory shifts by grade
+9. `tm_t_abnormality_by_worst_grade` - Worst post-baseline abnormalities
+10. `tm_t_exposure` - Exposure duration analysis
+11. `tm_t_abnormality` - Vital signs abnormalities
+12. `tm_t_mult_events` - Concomitant medications
+13. `tm_t_shift_by_arm` - ECG shifts by treatment arm
+14. `tm_t_shift_by_arm_by_worst` - ECG shifts by arm by worst grade
+15. `tm_t_pp_basic_info` - Patient profile basic information
+16. `tm_t_pp_laboratory` - Patient profile laboratory data
+17. `tm_t_pp_medical_history` - Patient profile medical history
+18. `tm_t_pp_prior_medication` - Patient profile prior medication
+19. `tm_t_ancova` - Analysis of covariance
+20. `tm_t_binary_outcome` - Binary outcome analysis
+21. `tm_t_coxreg` - Cox regression analysis
+22. `tm_t_logistic` - Logistic regression analysis
+23. `tm_t_glm_counts` - Generalized linear models for counts
+24. `tm_t_tte` - Time-to-event analysis
+25. `tm_a_gee` - Generalized estimating equations
+26. `tm_a_mmrm` - Mixed models for repeated measures
+
+### **Graphics Modules (tm_g_*) - 11 modules:**
+27. `tm_g_lineplot` - Line plots for time series data
+28. `tm_g_km` - Kaplan-Meier survival plots
+29. `tm_g_barchart_simple` - Simple bar charts
+30. `tm_g_ci` - Confidence interval plots
+31. `tm_g_forest_rsp` - Forest plots for response
+32. `tm_g_forest_tte` - Forest plots for time-to-event
+33. `tm_g_ipp` - Individual patient plots
+34. `tm_g_pp_adverse_events` - Patient profile adverse events plots
+35. `tm_g_pp_patient_timeline` - Patient profile timeline plots
+36. `tm_g_pp_therapy` - Patient profile therapy plots
+37. `tm_g_pp_vitals` - Patient profile vital signs plots
+
+### **General Modules**
+- `tm_front_page` - App information page
+- `tm_data_table` - Interactive data table
+- `tm_variable_browser` - Variable exploration
+
+## Key Features
+
+1. **Complete Coverage**: All 37 modules from `teal.modules.clinical`
+2. **Modular Design**: Each analysis type is contained in its own module
+3. **Interactive Filtering**: Global filters affect all modules
+4. **Consistent Interface**: All modules follow the same design patterns
+5. **CDISC Compliance**: Built for CDISC ADaM data standards
+6. **Clinical Focus**: Specifically designed for clinical trial analysis
+7. **Organized Sections**: Modules grouped by analysis type for easy navigation
+
+## Module Categories
+
+- **Adverse Events**: 5 modules (summary, by term, by grade, time-to-event, SMQ)
+- **Laboratory Data**: 3 modules (summary, shifts by grade, worst post-baseline)
+- **Patient Profiles**: 7 modules (basic info, lab, medical history, prior meds, plots)
+- **Statistical Analysis**: 8 modules (ANCOVA, binary outcome, Cox regression, logistic, GLM, TTE, GEE, MMRM)
+- **Graphics**: 11 modules (bar charts, CI plots, forest plots, KM plots, line plots, patient profiles)
+- **Exposure**: 2 modules (summary, duration)
+- **Vital Signs**: 1 module (abnormalities)
+- **Concomitant Medications**: 1 module (analysis)
+- **ECG Data**: 2 modules (shifts by arm, shifts by arm by worst)
+- **Demographics**: 1 module (summary)
+
+## Customization
+
+The app can be easily customized by:
+
+1. **Adding/Removing Modules**: Modify the `modules()` section
+2. **Changing Data**: Replace the data generation code with your own datasets
+3. **Adjusting Filters**: Modify the `teal_slices()` configuration
+4. **Customizing Variables**: Update the variable choices and selections
+
+## Dependencies
+
+- `teal`: Core framework
+- `teal.modules.general`: General purpose modules
+- `teal.modules.clinical`: Clinical trial specific modules (37 modules)
+- `random.cdisc.data`: Data generation
+- `dplyr`: Data manipulation
+- `nestcolor`: Color schemes
+- `sparkline`: Optional for enhanced graphics
+
+## Notes
+
+- The app uses simulated data for demonstration purposes
+- All modules include "Show R Code" functionality
+- Filters are applied globally across all modules
+- The app follows CDISC standards for clinical trial data analysis
+- Each module can be used independently in other applications
+- This is the most comprehensive demo of `teal.modules.clinical` available
+
+## Support
+
+For issues or questions:
+- Check the [teal documentation](https://insightsengineering.github.io/teal/)
+- Visit the [teal.modules.clinical documentation](https://insightsengineering.github.io/teal.modules.clinical/)
+- Report issues on the [GitHub repository](https://github.com/insightsengineering/teal.gallery/issues)