Clustering and Consensus Meta-Clustering
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Documentation for package ‘phynotype’ version 0.6.2
Help Pages
| phynotype-package | phynotype: Clustering Workflows and Consensus Meta-Clustering |
| adjusted_rand_index | Adjusted Rand Index |
| centers | Cluster centers |
| ceteris_paribus | Ceteris paribus profiles for clustering |
| cluster | Fit a clustering solution |
| clusters | Cluster assignments |
| explore | Explore clustering structure |
| feature_importance | Permutation feature importance for clustering |
| lime_explain | LIME-style local explanations for clustering |
| membership | Membership matrix |
| metacluster | Fit a consensus meta-clustering solution |
| method_used | Method used |
| mixed_distance | Compute a mixed-type distance matrix |
| n_clusters | Number of clusters |
| phynotype | phynotype: Clustering Workflows and Consensus Meta-Clustering |
| phynotype-scales | Discrete color/fill scales matching 'theme_phynotype' |
| plot_biplot | Plot a cluster biplot |
| plot_clusters | Plot clustered observations in 2D |
| plot_cluster_sizes | Plot cluster sizes |
| plot_coassoc | Plot the co-association matrix |
| plot_consensus | Plot consensus clustering in 2D |
| plot_dendrogram | Plot a clustering dendrogram |
| plot_feature_profiles | Plot feature profiles by cluster |
| plot_silhouette | Plot silhouette widths |
| predict.cluster_fit | Predict cluster assignments for new observations |
| prepare_mixed_data | Prepare mixed-type data for numeric clustering methods |
| prototypes | Cluster prototypes |
| scale_color_phynotype | Discrete color/fill scales matching 'theme_phynotype' |
| scale_fill_phynotype | Discrete color/fill scales matching 'theme_phynotype' |
| sizes | Cluster sizes |
| theme_phynotype | phynotype ggplot2 theme |
| validate | Validate clustering results |