Introduction | An Illustrative Example | Row Paths | Column Paths | Uniqueness of Paths | Wildcards In Paths | Operating On Tables With Paths | Column Counts | Section Dividers | Sorting Within An rtables Table | Extracting And Modifying Values | Footnotes | Table Structure And Technical Details | Row Structure | Label And Group Summary Rows | Column Structure

Introduction

Introduction | Who Are Your Numbers And What Do They Do? | There's Counting And Then There's Counting... | Denominators | "Yeah But What If" ... Conditionality In afuns | Conditionality Based On Column Facet | Conditionality Based On Row Facet | Why Not Both? | A Final Note On afun Complexity

Introduction | A Table Shell | A Brief Review Of rtables Layouts | Translating | Translating Column Structure | Translating Row Structure | Translating Cell Contents | Spanning Column Headers | Heterogeneous Column Structures (e.g., Risk Difference Columns) | Risk Difference Columns | Column-structure Aware Analysis Functions | Mixed Nesting Levels

Scope and Audience | Chapters

Introduction | A Brief Review | Split Function Basics | Default Faceting | Recognizing Non-Full-Factorial Faceting | Excluding Factor Levels | Adding Combination Levels | Nested Faceting On Non-Independent Variables | Facets That Vary Meaning Instead of Data Subset | Combining These Faceting Needs

Overview | List available templates | Generate a template for your own table | Notes | Customize the template

Overview | Prerequisite | The Workflow | Step 1: Initial Slide Generation | Step 2: Adding AI Footnotes | Example: Using a Local LLM | Step 3: Create the Final PowerPoint File | Appendix | Running Your Local LLM

Example of using tern.rbmi | The Data | Creating intercurrent event data | Draws | Define key variables | Impute | Analyze | Pool | Create output

Overview | Pattern A: autoslider Base Theme | Pattern B: Simple Theme Wrappers | Pattern C: Standalone Formats | How to Apply Your Custom Formats | Example: Visualize the output of your format implementation

Overview | Generating a Deck with append_all_slides | Example: Generating placeholder slides | Notes

Overview | Step 1: Write your template | Step 2: Create a softlink in inst/templates/ | Step 3: Verify with list_all_templates() | Step 4: Generate with use_template()

The Old Way | Setting column counts to visible at Layout time | Modifying counts on an existing table | Hiding counts | Higher Level Column Counts | Setting Column Counts to Visible at Layout Time | Manipulating Column Counts In An Existing Table | Setting individual column counts | Setting Col Count Visibility | Advanced Settings

Introduction | A Table In Need of Attention | Trimming | Trimming Rows | Trimming Columns | Pruning | Sorting | Sorting Fundamentals | Wildcards in Sort Paths | Sorting Within an Analysis Subtable | Writing Custom Pruning Criteria and Scoring Functions | Useful Functions and Accessors | Example Custom Scoring Functions | Sort by a character "score" | Sort by the Percent Difference in Counts Between Genders in Arm C

Introduction | Traditional Subsetting and modification with [ | Dealing with titles, foot notes, and top left information | Path Based Cell Value Accessing:

Advanced Customizations | Column Widths | Pagination | Horizontal separators (note section_div = <chr>)

tern Tabulation | tern Analyze Functions | Internals of tern Analyze Functions | Tabulation Examples | Demographic Table | Adverse Event Table | Statistics Functions | Response Table | Summary

Requirements | Workflow | The specifications specs.yml | The filters filters.yml | The functions | The backend machinery | Writing custom functions | create example function | Integrate it into the general workflow

Variable Class Conversion | Including Missing Values in rtables | Missing Values in Numeric Variables

For Developers

Mostly used | You may also try | Example | Reporting Bugs | Citing DEploid

Disclaimer | Creating an Example Table | Converting the Table to a Result Data Frame (ARD) | Customizing the Output | More Complex Outputs

Introduction | Referential Footnotes Workaround | Summary

GENERAL | General Concepts | 1. Input dataset and dataset names | 2. Expected variables in input analysis dataset | 3. Character vs Factor | 4. Testing the codes for plot generation | General Control Arguments | 1. lbl_overall: Column of Total | 2. Column counts: N=xxx | TABLES | Safety Summary (AET01) | 1. Safety Summary | 2. Safety Summary with Modified Rows | Safety Summary (Adverse Events of Special Interest) (AET01_AESI) | 1. Safety Summary (Adverse Events of Special Interest) | 2. Safety Summary (Adverse Events of Special Interest) (optional lines) | 3. Safety Summary (Adverse Events of Special Interest) (for studies with multiple drugs) | Adverse Events (AET02) | 1. Adverse Events | 2. Adverse Events (with High-level Term) | 3. Adverse Events (Preferred Terms only) | Adverse Events by Greatest Intensity(AET03) | 1. Adverse Events by Greatest Intensity | Adverse Events by Highest NCI CTCAE Grade (AET04) | 1. Adverse Events by Highest NCI CTCAE Grade | 2. Adverse Events by Highest NCI CTCAE Grade (Fill in of Grades) | 3. Adverse Events by Highest NCI CTCAE Grade with modified grouping of grade | Adverse Event Rate Adjusted for Patient-Years at Risk - First Occurrence (AET05) | 1. Adverse Event Rate Adjusted for Patient-Years at Risk - First Occurrence | 2. Adverse Event Rate Adjusted for Patient-Years at Risk - First Occurrence (setting type of confidence interval) | Adverse Event Rate Adjusted for Patient-Years at Risk - All Occurrences (AET05_ALL) | 1. Adverse Event Rate Adjusted for Patient-Years at Risk - All Occurrences | 2. Adverse Event Rate Adjusted for Patient-Years at Risk - All Occurrences (setting type of confidence interval) | Most Common (>=5%) Adverse Events (AET10) | 1. Most Common (>=5%) Adverse Events | 2. Most Common (>=8%) Adverse Events (setting threshold) | Absolute Value and Change from Baseline by Visit (CFBT01) | 1. Absolute Value and Change from Baseline by Visit | 2. Absolute Value and Change from Baseline by Visit without Screening | 3. Absolute Value by Visit | Concomitant Medications by Medication Class and Preferred Name (CMT01A) | 1. Concomitant Medications by Medication Class and Preferred Name | 2. Concomitant Medications by Medication Class and Preferred Name (changing ATC class level) | 3. Concomitant Medications by Medication Class and Preferred Name (classes sorted by frequency) | 4. Concomitant Medications by Medication Class and Preferred Name (total number of treatments per medication class suppressed) | Concomitant Medications by Preferred Name (CMT02_PT) | 1. Concomitant Medications by Preferred Name | Cox Regression (COXT01) | 1. Cox Regression | 2. Cox Regression (with interaction term) | 3. Cox Regression (specifying covariates) | 4. Cox Regression (setting strata, ties, and alpha level) | Multi-variable Cox Regression (COXT02) | 1. Multi-variable Cox Regression | 2. Multi-variable Cox Regression (specifying covariates) | 3. Multi-variable Cox Regression (setting strata, ties, and alpha level) | Demographics and Baseline Characteristics (DMT01) | 1. Demographics and Baseline Characteristics with All Patients | 2. Demographics and Baseline Characteristics without All Patients | 3. Demographics and Baseline Characteristics with an additional study specific continuous variable | 4. Demographics and Baseline Characteristics with an additional study specific categorical variable | 5. Demographics and Baseline Characteristics with additional vital signs baseline values from ADVS or ADSUB | Patient Disposition (DST01) | 1. Patient Disposition | 2. Patient Disposition (with grouping of reasons) | 3. Patient Disposition (adding end of treatment status) | 4. Patient Disposition (adding details of study ongoing status) | Deaths (DTHT01) | 1. Deaths | 2. Deaths (adding "Primary Cause of Death" details for 'Other' category) | 3. Deaths (adding summary by days from last study drug administration) | ECG Results and Change from Baseline by Visit (EGT01) | 1. ECG Results and Change from Baseline by Visit | ECG Abnormalities (Regardless of Abnormality at Baseline) (EGT02_1) | 1. ECG Abnormalities (Regardless of Abnormality at Baseline) | ECG Abnormalities (Among Subject Without Abnormality at Baseline) (EGT02_2) | 1. ECG Abnormalities (Among Subject Without Abnormality at Baseline) | Shift Table of ECG Interval Data - Baseline versus Minimum/Maximum Post-Baseline (EGT03) | 1. Shift Table of ECG Interval Data - Baseline versus Minimum Post-Baseline | 2. Shift Table of ECG Interval Data - Baseline versus Maximum Post-Baseline | ECG Actual Values and Changes from Baseline by Visit (EGT05_QTCAT) | 1. ECG Actual Values and Changes from Baseline by Visit | 2. ECG Actual Values and Changes from Baseline by Visit (removing default analyses) | Study Drug Exposure (EXT01) | 1. Study Drug Exposure | Laboratory Test Results and Change from Baseline by Visit (LBT01) | 1. Laboratory Test Results and Change from Baseline by Visit | 2. Laboratory Test Results and Change from Baseline by Visit (customized precision) | Laboratory Abnormalities (LBT04) | 1. Laboratory Abnormalities | Laboratory Abnormalities with Single and Replicated Marked (LBT05) | 1. Laboratory Abnormalities with Single and Replicated Marked | 2. Laboratory Abnormalities with Single and Replicated Marked showing all categories | 3. Laboratory Abnormalities with Single and Replicated Marked with study specific MLAs | Laboratory Abnormalities by Visit and Baseline Status (LBT06) | 1. Laboratory Abnormalities by Visit and Baseline Status | Laboratory Test Results with Highest NCI CTCAE Grade Post-Baseline (LBT07) | 1. Laboratory Test Results with Highest NCI CTCAE Grade Post-Baseline | Laboratory Test Results Shift Table - Highest NCI-CTCAE Grade Post-Baseline by Baseline NCI-CTCAE Grade (LBT14) | 1. Laboratory Test Results Shift Table - Highest NCI-CTCAE Grade Post-Baseline by Baseline NCI-CTCAE Grade (High) | 2. Laboratory Test Results Shift Table - Highest NCI-CTCAE Grade Post-Baseline by Baseline NCI-CTCAE Grade (Low) | 3. Laboratory Test Results Shift Table - Highest NCI-CTCAE Grade Post-Baseline by Baseline NCI-CTCAE Grade (High) Without Patients with Missing Baseline | 4. Laboratory Test Results Shift Table - Highest NCI-CTCAE Grade Post-Baseline by Baseline NCI-CTCAE Grade (Low) with Missing Baseline Considered as Grade 0 | 4. Laboratory Test Results Shift Table - Highest NCI-CTCAE Grade Post-Baseline by Baseline NCI-CTCAE Grade (with fill in of grades) | Medical History (MHT01) | 1. Medical History | 2. Medical History showing additional column 'All Patients' | Major Protocol Deviations (PDT01) | 1. Major Protocol Deviations | Reasons for Major Protocol Deviations Related to Epidemic/Pandemic (PDT02) | 1. Reasons for Major Protocol Deviations Related to Epidemic/Pandemic | Duration of Exposure for Risk Management Plan (RMPT01) | 1. Duration of Exposure for Risk Management Plan | Extent of Exposure by Age Group and Gender for Risk Management Plan (RMPT03) | 1. Extent of Exposure by Age Group and Gender for Risk Management Plan | Extent of Exposure by Ethnic Origin for Risk Management Plan (RMPT04) | 1. Extent of Exposure by Ethnic Origin for Risk Management Plan | Extent of Exposure by Race for Risk Management Plan (RMPT05) | 1. Extent of Exposure by Race for Risk Management Plan | Best Overall Response (RSPT01) | 1. Best Overall Response | 2. Best Overall Response (Ordering of treatment groups) | 3. Best Overall Response (selecting sections to display) | 4. Best Overall Response (with stratified analysis) | 5. Best Overall Response (modifying analysis details like type of confidence interval, alpha level, test for p-value) | 6. Best Overall Response (modifying the definition of overall response) | Time-to-event Summary (TTET01) | 1. Time-to-event Summary | 2. Time-to-event Summary (selecting sections to display) | 3. Time-to-event Summary (modifying analysis details like confidence interval type, ties, and alpha level) | 4. Time-to-event Summary (with stratified analysis) | 5. Time-to-event Summary (modifying time point for the "survival at xx months" analysis) | 6. Time-to-event Summary (modifying the p-value method for testing hazard ratio) | Vital Signs (VST01) | 1. Vital Sign Results and Change from Baseline by Visit | Vital Signs Abnormalities (Regardless of Abnormality at Baseline) (VST02_1) | 1. Vital Sign Abnormalities (Regardless of Abnormality at Baseline) | Vital Signs Abnormalities (Among Subject Without Abnormality at Baseline) (VST02_2) | 1. Vital Sign Abnormalities (Among Subject Without Abnormality at Baseline) | LISTINGS | Glossary of Adverse Event Preferred Terms and Investigator-Specified Terms (AEL01_NOLLT) | 1. Glossary of Adverse Event Preferred Terms and Investigator-Specified Terms | Graphics | Forest Plot for Odds Ratio (FSTG01) | 1. Forest Plot for Odds Ratio (with subgroup analysis) | 2. Forest Plot for Odds Ratio (with a user-defined confidence level) | 3. Forest Plot for Odds Ratio (with p-values and/or different statistics) | 4. Forest Plot for Odds Ratio (with user-defined subgroup analysis) | 5. Forest Plot for Odds Ratio (with stratified analysis) | 6. Forest Plot for Odds Ratio (without proportional sizing of the odds ratio symbol) | Forest Plot for Hazard Ratio (FSTG02) | 1. Forest Plot for Hazard Ratio (with subgroup analysis) | 2. Forest Plot for Hazard Ratio (with p-values and/or different statistics) | 3. Forest Plot for Hazard Ratio (with user-defined subgroup analysis) | 4. Forest Plot for Hazard Ratio (with stratified analysis) | 5. Forest Plot for Hazard Ratio (without proportional sizing of the hazard ratio symbol) | Kaplan-Meier Plot (KMG01) | 1. Kaplan-Meier Plot (without comparative statistics) | 2. Kaplan-Meier Plot (with comparative statistics) | 3. Kaplan-Meier Plot (without censoring marks) | 4. Kaplan-Meier Plot (without estimation of median survival time) | 5. Kaplan-Meier Plot (with statistical annotation of either median or min of survival time) | 6. Kaplan-Meier Plot (without the table of patients at risk) | Mean Plot (MNG01) | 1. Plot of Mean and Confidence Interval (with Table Section) | 2. Plot of Mean and Confidence Interval of Change from Baseline of Vital Signs | 3. Plot of Mean (+/-SD) (Changing the Statistics) | 4. Plot of Mean and Confidence Interval (Modify Alpha Level) | 5. Plot of Mean and Confidence Interval （With Number of Patients Only) | 6. Plot of Mean and Confidence Interval (without Table Section)

Common Clinical Trials Analyses | Analytical Functions for rtables | Clinical Trial Visualizations | Interactive Apps | Summary

Introduction | Getting Started | Content Information | Summary

Introduction | Getting Started | Nested Tables | NA Values | Custom Aggregation | Marginal Summaries | Table Decorations | Summary

Controlling Facet Levels | Provided Functions | Controlling Combinations of Levels Across Multiple Variables | trim_levels_in_group | trim_levels_to_map | Combining Levels | add_overall_level | add_combo_levels | Fully Customizing Split (Facet) Behavior | An Example Custom Split Function | An Illustrative Example of A Custom Split Function | Overriding the Core Split Function | Design of Pre- and Post-Processing Functions For Use in make_split_fun

Rows and cell values alignments | Top-left Materials | Table Inset | Horizontal Separation | Section Dividers | Indent Modifier | Variable Label Visibility | Cell, Label, and Annotation Wrapping | Cell & Label Wrapping | Title & Footer Wrapping

Introduction | Demographic Table | Variations on the Demographic Table | Using Layouts | Adverse Events | Adverse Events By ID | Adverse Events By ID and By Grade | Response Table | Time to Event Analysis Table

Introduction | Data Pre-Processing | Creating Helper Functions: Cox Regression Model Calculations | tidy Method for summary.coxph Objects: tidy.summary.coxph | Function to Estimate Interaction Effects: h_coxreg_inter_effect | Function to Extract Effect Information: h_coxreg_extract_interaction | Creating a Helper Function: cached_model | Creating the Analysis Function: a_cox_summary | Selecting Parameters | Constructing the Table

Introduction | Overview | Data | Building a Table | Quick Start | Layout Instructions | Adding Column Structure | Adding Row Structure | Adding Group Information | Comparing with Other Tabulation Frameworks | Summary

Introduction | Getting Started | Detailed Table Structure | Insights on Value Format Structure | Applications | Summary

Introduction | Building A Table Row By Row | Tabulation With Row Structure | Calculating the Mean | Group Summaries | Pattern III

Titles and Non-Referential Footer Materials | Page-by splitting | Referential Footnotes | Adding Cell- and Analysis-row Referential Footnotes At Tabulation Time | Annotating an Existing Table with Referential Footnotes

Introduction | Default Formatting in as_listing | Column-Wise Formatting in as_listing | Adding Formatted Columns to a Listing via add_listing_col | Summary

Introduction | Descriptive Statistics | Methodology | Statistical model | Estimation | Inference | Covariance structure | Model fitting | Setup | Model fitting via tern.mmrm | Model fitting manually in R | Model fitting via SAS | Diagnostics | Residual analysis | Outlook

Introduction | Basics of Pagination | Alternative Methods to Specify Page Size | 1. pg_width and pg_height | 2. lpp and cpp | 3. colwidths | Pagination with Exporters | export_as_txt | export_as_rtf | Pagination by Parameter | Combining Pagination by Parameter with Regular Pagination | Combining Pagination by Parameter with export_as_txt | Summary

Introduction | Building a Listing | Key Columns | Titles and Footers | Summary

Getting Started | Code Maintenance | Update Cached Data

Introduction | The Formatting Map Structure | Calling reformat | Example | Rule Attributes

formatters | Formatting values | Format labels | Table Rendering Framework

Introduction | Example | Setup | Model Fitting | Tabulation

NOTE | Control splitting with provided function (limited customization) | Custom Split Functions | Adding an Overall Column Only When The Split Would Already Define 2+ Facets | Leveraging .spl_context | What Is .spl_context? | Different Formats For Different Values Within A Row-Split | Simulating 'Baseline Comparison' In Row Space

Introduction | TLG-functions | preprocessing | postprocessing | Example AET02 | chevron_tlg object customization | Custom chevron_tlg object creation

Introduction | Using a chevron-defined object | With a modified chevron object

Introduction | Row Splitting

Formats Precedence | Format Precedence and Inheritance Rules | Standard Format | Cell Format | Parent Table Format and Inheritance | NA Handling | Replacing NA Values at the Cell Level | Parent Table Replacement of NA Values and Inheritance Principles

Overview | Simple Example

tern Formatting Functions Overview | Comparing tern & formatters Formats | Formatting Function Basics | Number of Decimal Places to Display | Value Thresholds | Creating Custom Formatting Functions | Summary

Introduction | Main Features | A Simple Example