Cardinal comes with a walkthrough vignette that demonstrates many of its basic and advanced functionalities on simulated datasets.

The companion data package CardinalWorkflows includes vignettes that work through specific workflows (clustering, classification, etc.) on real data.

DOCUMENTATION

• Cardinal v3 user guide
• Cardinal v3 statistical methods
• Reference manual

UNSUPERVISED ANALYSIS

• Clustering workflow vignette
• Examples: Whole Pig Fetus Cross-Section, Cardinal Oil Painting
• PCA (Principal Components Analysis)
• Spatially-aware k-means clustering
• Spatial Shrunken Centroids clustering

SUPERVISED ANALYSIS

• Classification workflow vignette
• ​Examples: Human Renal Cell Carcinoma (RCC)
• PLS-DA (Projection to Latent Structures Discriminant Analysis)
• O-PLS-DA (Orthogonal PLS-DA)
• Spatial Shrunken Centroids classification
• Cross-validation

STATISTICAL TESTING

• Testing workflow vignette
• ​Examples: Human Renal Cell Carcinoma (RCC)
• Spatial-DGMM (Spatially-aware Dirichlet Gaussian Mixture Model)
• Linear model-based statistical testing