Two APIs: legacy vs. Self-describing | Legacy API (parseOTBFunction() / runOTB()) | Self-describing API (recommended) | Minimal workflow (Self-describing) | Typical transparent workflow (Self-describing) | Example: DimensionalityReduction (PCA) | Legacy workflow (supported but not recommended) | What changed (Self-describing) | Compatibility and deprecations | Compatibility | Deprecations (explicit list)

Vignette scope | Windows | Recommended baseline: OSGeo4W | Express installation (minimal) | Advanced installation (recommended) | Important note: starting R/RStudio | Orfeo Toolbox (Windows) | Linux | Baseline: use distribution packages where possible | Ubuntu / Debian | Orfeo Toolbox (Linux) | Note on SAGA versions | Arch Linux | Fedora | macOS | GDAL | GRASS | SAGA | QGIS | Homebrew | Practical guidance: “default” vs. “anything else”

What is link2GI? | Why link2GI? | What does “linking” mean? | GRASS GIS | SAGA GIS | Orfeo Toolbox (OTB) | GDAL

Motivation | Design Goals | Core Concept: The GDAL Context | Creating a Context from linkGDAL() | Inspecting Capabilities (Fingerprinting) | Running GDAL Commands Deterministically | Help-Driven Skeleton Generation | Building Arguments Programmatically | NDJSON Logging for Reproducibility | Relationship to Existing Packages | When Is This Useful? | Summary

Brute force search | Setting up project structures | linkSAGA - Find and set up 'SAGA' API bindings | Find and set up GRASS 7/8 API bindings | Important note: GRASS runtime environment | Windows (OSGeo4W) | Linux | macOS | linkGRASS | Standard full search usage | Typical for specified search paths and OS | Specific examples | Manual version selection | Creating a permanent gisdbase folder | Using a permanent gisdbase folder | Manual Setup of the spatial attributes | A typical use case for the Orfeo Toolbox wrapper | Usecases presented on the GEOSTAT August 2018 | Find slides and materials | The examples

Real world example | Downloading census data | Preprocessing the data | Setting up a GRASS project | Importing raster data into GRASS | Importing data as GRASS vector points

Using the RStudio GUI | Console Best-Practice Workflow | Minimal recommended lifecycle | Ad 1 - Project creation | Ad 2 - Project entry point | Comprehensive Workflow Description and Design Principles | Scope of initProj() in link2GI | Separation of responsibilities: initProj() vs setupProj() | initProj() | setupProj() | Default setups and configuration-driven structure | Creating a project from the console | Customising a project at creation time | Location tags (loc_name) | The role of src/functions/000_setup.R | Template system and file generation | Common failure modes