Working pharmaRTF Into Your Process | A Small Note | How It Works | Custom Reader Functions | Putting It Together | Further Reading

Metadata Settings

The decimal data type | Decimal Data Type | A note on digits

Bulk File Conversion

fileOID

Using datasetjson | Writing and Reading | NDJSON | Compressed files | Working with the metadata

Empty Value Formatting | Auto Precision | Overall Precision Maximums | External Precision | Parenthesis Hugging

Default Layer Formats | Precision Cap | Overall Precision Maximum | Custom Summaries | Scientific Notation | Quantile Algorithms | IBM Rounding

How tplyr2 Works | The tplyr_spec() Object | The tplyr_layer() Object | Building a Table | String Formatting in tplyr2 | Layer Types | Descriptive Statistics Layers | Multiple Target Variables | Count Layers | Total Rows | Distinct Counting | Nested Counts | Shift Layers | Numeric Data | Where to Go from Here | References

Introduction | Small and Large Percentages | Zero Counts | Showing Only Selected Levels | Missing and Total Rows | One Statistic Per Column | Count layers: stat_columns | Descriptive layers: stats_as_columns | Shift Table Denominators | The denominator row | Indenting and Wrapping Nested Terms | Conventions a Format String Cannot Express | Getting the Table Out | Where to Go From Here

Introduction | A Simple Count | Adding a Total Column | Custom Column Groups | Custom Format Strings | Total Rows | Population Data: Getting the Denominator Right | Distinct Versus Event Counts | Displaying Statistics in Separate Columns | A Note on Parenthesis Hugging | Nested Count Summaries | Collapsing Row Labels | Default Mode (Stub Rows) | Nest Mode | Nested Counts with Total Rows | Where to Go from Here

Introduction | Built-in Summaries | Quantile Algorithm | Custom Summaries | Layer-Level Custom Summaries | Session-Level Custom Summaries | Overriding Built-in Summaries | Multi-Variable Descriptive Statistics | Records Assessed: n Versus n_records | Statistics as Columns | Adding a Comparison p-value | Where to Go From Here

Introduction | Seeing the alignment in this vignette | Anatomy of a Format String | Literals cannot contain x, X, a, or A | Field Width and Padding | Where Format Strings Go | Count and shift layers: the n_counts key | Descriptive statistics layers: a named list, one entry per row | Analyze layers: whatever your function returns | One format string per column: stat_columns | Statistic Keywords by Layer Type | Count and shift layers | Descriptive statistics layers | Rounding | Missing Values and the empty Argument | Formatting Numbers Outside a Layer | Where to Go From Here

Why Traceability Matters | Building with Metadata | Row IDs | Inspecting Cell Metadata | Getting Source Data | Metadata for Count Layers | Total Rows | Metadata for Descriptive Statistics Layers | Where Filters in Metadata | Anti-Join Metadata for Missing Subjects | Stat Columns and the statistic Field | Practical Applications | Summary | See Also

Introduction | Building the Example Data | Row Masks | Adding Row Breaks Between Layers | Collapsing Row Labels | Extracting Numeric Values | Conditional Formatting | Replacing Leading Whitespace | Standalone Format Application | Text Wrapping | Putting It All Together | Adding Conditional Formatting to the Pipeline | Collapsing In Place (Nest Mode) | The Final Step: as_display() | Summary

Introduction | Auto-Precision | The +N offset | precision_on: measuring a different variable | precision_by: one width per group | Capping Precision | Supplying Precision From Outside | Auto-precision is a descriptive-statistics feature | Parenthesis Hugging | Hugging is applied per group, not per side | There must be something to hug | Migrating from Tplyr v1 | Hugging with auto-precision | Putting It Together | Where to Go From Here

Introduction | Basic Risk Difference | Configuring Comparisons | Formatting Output | Confidence Interval Level | Risk Difference with Distinct Counts | Interaction with Special Rows | Extracting Raw Numbers | Risk Difference Versus Association Tests | Summary | Single-Level Layers Only

Introduction | A Basic Example | Filling Missing Groups Using Factors | Customizing the Format | Shift Denominators | The Denominator Row | Zero Cells and Percent Thresholds | Distinct (Subject-Level) Shifts | Association Tests | One Thing to Note | Where to Go From Here

Introduction | Ordering Columns Explained | Sorting Across Layers | Sorting by Variable Values | Factor Level Ordering | VARN Companion Column Ordering | Sorting Descriptive Statistics | Sorting Count Layers | Sorting by Count | Nested Count Sorting | Sorting Preferred Terms by Frequency | Practical Example: Preparing a Final Table

Introduction | Column Variables | Multiple Column Variables | Table-Level Filtering with where | Treatment Groups | Total Groups | Custom Groups | Combining Total and Custom Groups | Population Data | Extracting Header N | Population Data with Filters | Data Completion | Limiting Completion with limit_data_by | Where to Go From Here

Introduction | Viewing Current Options | IBM Rounding | Quantile Algorithm | Precision Cap | Custom Summaries | Scientific Notation Control | Reading Variable Labels | Resetting Options | See Also

Introduction | Converting to ARD | ARD Structure | Count Layer ARD | Descriptive Statistics Layer ARD | Reconstructing from ARD | Verifying the Round-Trip | Use Cases | Standards-Compliant Data Exchange | Separating Computation from Presentation | Layer Coverage | Archiving and Reproducibility | Summary

Introduction | The Population Principle | Step 1: Incidence by System Organ Class and Preferred Term | Step 2: "Any Adverse Event" and Subjects With No Events | Step 3: A Between-Arm Comparison | Step 4: A "Most Frequent Events" Variant, With Risk Difference | Step 5: A Display-Ready Table | See Also

Where statistics come from in tplyr2 | Native comparisons across the treatment columns | Risk difference | Association tests with assoc_test() | Single-proportion confidence intervals | Bringing your own statistics | Attach a statistic as a column | Attach a statistic as a row | Missing or non-estimable results | group_analyze() for in-spec custom statistics | Handing off to a table package

Introduction | The analyze_fn Contract | Format Strings Mode | Multiple Statistics Per Row | Pre-Formatted Mode | Integration with by Variables | Combining with Other Layers | Error Handling | Summary | See Also

Introduction | Default Behavior | Controlling Denominator Grouping with denoms_by | Separate Denominator Populations with denom_where | Excluding Values from Denominators with denom_ignore | Denominators with Distinct Counts | Confidence Intervals for the Single Proportion | Denominators with Population Data | Missing Subjects | Putting It All Together | Summary | See Also

Introduction | Quick Reference: Function Mapping | Key Differences in Detail | Data Is Separated from Configuration | Variable Names Are Quoted Strings | Settings Are Collected in an Object | Format Strings Use Quoted Variable Names | Side-by-Side Examples | Demographics Table | Tplyr v1 | tplyr2 | Adverse Events Table (Nested Counts) | New Features in tplyr2 | Comparative and Inferential Statistics | Binding External Results and Display Helpers | Multi-Column Count Layouts | Spec Serialization | Custom Analysis Layers | Cell-Level Metadata | ARD Conversion and Numeric Data | Performance | Overall Speedup by Layer Type | Detailed Results | Count Layers | Nested Count Layers | Descriptive Statistics Layers | Shift Layers | Summary

Introduction | Writing a Spec to JSON | Reading a Spec Back | YAML Format | What Gets Serialized | Expressions | Format Strings | Labels in by | Functions | Layer Settings | Examining the Serialized Output | A More Complex Example | Use Cases | Version-Controlled Table Definitions | Sharing Across Teams | Applying a Spec to Different Data | Regulatory Archival | See Also

Basics | Titles and Footnotes | Pagination and Alternating Pages | Column Headers and Widths | Writing to DOCX | Why this framework?

Creating Setting Functions | clinify_docx_default | clinify_titles_default and clin_footnotes_default() | clinify_table_default | clinify_grouplabel_default | clinify_caption_default | Applying the Options

Titles and footnotes from a spec | Footnote Pages

Introduction | {abba} Design | Prerequisites | Create the API | Deploy the API | Connect Setup | API Access | API Runtime | Test it Out | Troubleshooting

End User Facing Functions | Create a Scheduled Batch File | Deployment Prep | Deploy a Batch File to Connect | Schedule Your Cron Job

Submit a Job | Get Job Status | Get the Log Content | Submit a batch of jobs to SLURM cluster

End User Facing Functions | Create a batch list from dataset

Submit a Job | Get Job Status | Get the Log Content

Submit a Job | Get Job Status | Get the Log Content | Interacting with Kubernetes

Built-in Summaries | Notes About Built-in's | Custom Summaries

Population Data in the Denominator | Denominator Grouping | Count layers | Shift layers | Controlling the Denominator Filter | Missing Counts | Missing Subjects | Adding a 'Total' Row

Basic Templates | Templates With Parameters | Viewing and Removing Templates

A Basic Example | Filling Missing Groups Using Factors | Where to go from here

Overview of Authentication Methods | API Key Authentication | When to Use It | When to Avoid It | OAuth 2.0 Authorization Code Flow | Initial Setup | Authorizing | Token Refresh | OAuth 2.0 Resource Owner Password Flow | Setup | Using Environment Variables | Important Limitations | Choosing the Right Method | How Authentication State is Stored | Token Expiration | Troubleshooting | Next Steps

Getting an API Key | If You're an Admin | If You're Not an Admin | Setting Up Your Credentials | Using Environment Variables | Setting Environment Variables | Verifying Your Setup | A Note on Security | Next Steps

Prerequisites | Downloading Files | Basic Usage | Downloading to a Temporary File | Understanding Egnyte Paths | Uploading Files | Handling Existing Files | Creating Folders | Working with Different File Types | Listing Directory Contents | Recursive Listing | Filtering Results | Combining with Downloads | Common Patterns | Downloading, Processing, and Re-uploading | Batch Downloads | Checking If a File Exists Before Uploading | Error Handling | Next Steps

Prerequisites | Reading Data Files | CSV Files | Delimited Files | Excel Files | SAS Files | Stata Files | SPSS Files | R Objects (RDS) | Writing Data Files | SAS Transport Files | Optional Dependencies | A Few Tips | Working with Large Files | Passing Arguments Through | File Extensions Matter | Comparison with Base File Transfer | Next Steps

clin_auto_page() | clin_page_by() | clin_group_by() | clin_alt_pages()

A Simple Example | Distinct Versus Event Counts | Nested Count Summaries

Build a tplyr_meta object | Building your own metadata table | Anti-joins | Appending Existing Tplyr Metadata | Metadata Without Tplyr | Tying it Together

Format Strings | General Formatting | Controlling Formatting | Lowercase 'x' | Uppercase 'X' | Auto-precision

Generating the Metadata | Extracting The Input Source | Extracting a Result Cell's Metadata | Anti Joins

String wrapping | Row Masking | Collapsing Row Labels | Leading Spaces in HTML Files | Conditional Formatting | Extracting a Format Group | Highly Customized Sort Variables | External Data Formatting

Table Parameters | Additional Treatment Groups | Population Data | Data Completion | Where to Go From Here

How Tplyr Works | The tplyr_table() Object | The tplyr_layer() Object | Adding Layers to a Table | A Note Before We Go Deeper | Constructing Layers | String Formatting in Tplyr | Layer Types | Descriptive Statistic Layers | Count Layers | Shift Layers | Where to go from here? | References

Introduction | A Small Note | Understanding Document Orientation Within pharmaRTF | Multi-level Column Headers | Minimizing Cell Padding | Setting Spacing Between Column Headers and Titles | Split Titles | Special Title/Footnote Formats | PAGE_FORMAT: | DATE_FORMAT: | FILE_PATH: | Further Reading

Notes | Introduction | A Small Note | Huxtable Basics | Changing Table Shape | Column Headers | Cell Formatting | Cell Merging | Some Final Notes | Further Reading

Version 0.1.1 updates | What is pharmaRTF? | A Small Note | The Basics | Further Reading