Compression by Default | What Gets Compressed | Choosing a Codec | Gzip | Zstandard and LZ4 | Blosc2 and Bitshuffle | Szip | Legacy Codecs | Comparing Codecs on Your Own Data | Sharing Files with Other Software | Lossy Compression | ZFP | Scale-Offset: int_packing and float_rounding | Blosc2 Truncate Precision | The Filter Pipeline | Shuffling | Blosc2 Delta | Checksums | Rules and Automatic Adjustments | Chunking | Inspecting the Results | Compression String Reference

Supported Data Types | Dimensions: Scalars, Vectors, and Arrays | Numeric Data | 64-bit Integers (integer64) | Double (Numeric) Data | Logical Data | Character Data | Variable-Length: | Fixed-Length: | Dates and Times (POSIXt) | Complex Data | Raw Data | Factors | Lists | Data Frames | NULL | Data Types and Compression

HDF5 for R Users | Basic Usage | Writing Numeric Data | Reading Data | Data Type Mapping | Complex Data Structures | Lists as Groups | Data Frames as Compound Datasets | Attributes | File Inspection | Compression | Reading Part of a Dataset | Learn More

Basic Usage | Scalars vs. 1D Arrays | Numeric and Logical Data | Automatic Type Selection | Handling Missing Values (NA) | Forcing Specific Types | Character Vectors (Strings) | Variable-Length | Fixed-Length | Compression | 64-bit Integers

Basic Usage | Customizing Column Types | Row Names | Compression and Partial Reading

Writing Matrices | Writing N-Dimensional Arrays | Dimension Names (dimnames) | Dimension Ordering (Row-Major vs. Column-Major) | How h5lite handles it | Interoperability with Python | Chunking and Compression | Partial Reading

Why Partial Reading Matters | The HDF5 Storage Model: Chunking and Compression | Designing for Partial Reading | Memory Efficiency of start and count | The "Smart" start Parameter | Single-Value Examples | Dimension Simplification (Exact vs. Range Indexing) | Drilling Down: Multi-Value start and N-Dimensional Arrays

Introduction | Input Data | Weighted vs Unweighted Metrics | Formulas | Abundance-Based (Weighted) | Presence / Absence (Unweighted) | Phylogenetic | Partial Calculation | References

Introduction | Alpha Diversity | Beta Diversity | Example | Rarefaction | Classic Metrics | Phylogenetic Metrics | Distance Matrices | Performance with Large Datasets

The Hierarchical Model | Creating Groups | Implicit Creation (Recommended) | Explicit Creation | Using Lists as Groups | Inspecting Structure | Moving and Renaming | Deleting Objects

Optimizing ecodive for Large Datasets | The Optimal Input: Compressed Sparse Matrices | Why Sparse Matrices? | rbiom Users | Handling Data Transformations | The Exception: Centered Log-Ratio (CLR) | Summary

Input Matrix | Richness Metrics | Diversity Metrics | Dominance Metrics | Phylogenetic Metrics | Formulas | Abundance-based Coverage Estimator (ACE) | Faith's Phylogenetic Diversity (Faith's PD)

Writing Attributes | 1. Explicit Writing | 2. Implicit Writing (R Attributes) | Reading Attributes | 1. Accessing Specific Attributes | 2. Reading with the Dataset | Managing Attributes | Listing Attributes | Deleting Attributes | Important Limitations | 1. No Dimension Scales (Loss of Names) | 2. No Attributes on Attributes (Nesting) | Controlling Attribute Types | Customizing Storage Type | Customizing Read Type | Special Note: Dimensions

Basic Usage | Navigation and Working Directories | Reference Semantics | Closing the Handle | Method Reference

The Safety Rule: Always Lock | Recommended Strategy: File Locking with flock

Reacting to Results | Output vs Result | Reformatting Output | Transformation | job Details | Non-blocking | Signaling Errors | Promise Handling

Setup | Introduction | A Callback Function | Triggers | Special Triggers | jobqueue States | worker States | job States | Attaching | Removing | Default job Hooks | Use Case: Priority Setting | Use Case: Rate Limiting

Introduction | Expressions | Variables | Functions | Example

Create a jobqueue | Create a job | Access the Result | Add a Callback Hook | Interrupt Evaluation | Passing Data

Introduction | Setup | Immediate Stop | Interrupting with $stop() | Assigning to $output | Replacing and Combining | Stop ID | Copy ID | In jobqueue() | Timeouts