Introduction | A minimal example | Structure of a phylospatial object | Phylogeny | Community matrix | Spatial data | Starting from occurrence points | A realistic example | Non-phylogenetic data | Tree scaling | Affine rescaling | Differential transforms

The basics | Controlling the view | 3D layers | Surfaces | Points | Paths | Prisms | Hulls | Distributions | Text | Lighting | Scales, guides, and themes | Z-axis scales | Shaded guides | Panels and themes | Annotations | Mixing 2D and 3D | Interactivity & animation

Introduction | Greedy stepwise prioritization via ps_prioritize() | Performance curves | Probabilistic prioritization | Conservation benefit functions | Optimization with ps_prioritizr()

What is circuit-theory connectivity? | Installation | Key Inputs | The resistance surface | Focal nodes | Choosing a Mode | Circuitscape: Pairwise Mode | Circuitscape: One-to-All and All-to-One Modes | Circuitscape: Advanced Mode | Additional Circuitscape Options | Per-pair current and voltage maps | Variable source strengths | Short-circuit regions | Include/exclude pairs | Omniscape: Moving-Window Connectivity | With source strength weights | Conditional connectivity | Parallel processing | Performance | Saving Outputs | Tips

Diversity measures | Null model randomization | Spatially constrained randomization | CANAPE

Dissimilarity | Distance decay | Ordination | Regionalization

Introduction | Use cases | Categorical null models | Available algorithms | Example: Basic categorical randomization | Understanding fixed margins | Quantitative null models | Example: Basic quantitative randomization | Stratification options | Controlling what's preserved | Efficient repeated randomization | Convergence diagnostics | Weighted pair sampling | Basic usage: spatial constraints on rows | Hard thresholds as soft strata | Column weights | Dual-margin weighting | Integration with vegan | References | Further reading