Taxonomic Diversity Indices Using Deng Entropy
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Documentation for package ‘taxdiv’ version 0.1.0
Help Pages
| anatolian_trees | Anatolian Forest Trees: Multi-Site Species Data |
| avtd | Average Taxonomic Distinctness (Delta+) |
| batch_analysis | Batch Analysis from a Single Data Frame |
| build_tax_tree | Build a Taxonomic Tree from Species Data |
| compare_indices | Compare All Diversity Indices Side by Side |
| delta | Taxonomic Diversity Index (Delta) |
| delta_star | Taxonomic Distinctness (Delta*) |
| deng_entropy_level | Calculate Deng Entropy at a Single Taxonomic Level |
| gazi_comm | Example Community Vector: 8 Anatolian Tree Species |
| gazi_gytk | Example Taxonomy: 8 Anatolian Tree Species |
| ozkan_pto | Calculate Ozkan's Taxonomic Diversity Index (pTO) |
| ozkan_pto_full | Full Ozkan pTO Pipeline (Islem 1 + 2 + 3) |
| ozkan_pto_jackknife | Jackknife Analysis for Ozkan's pTO Index (Islem 1 / Run 1) |
| ozkan_pto_resample | Stochastic Resampling of Ozkan's pTO Index (Islem 2 / Run 2) |
| ozkan_pto_sensitivity | Sensitivity Analysis of Ozkan's pTO Index (Islem 3 / Run 3) |
| plot_bubble | Bubble Chart of Species Contributions to Diversity |
| plot_funnel | Funnel Plot for AvTD/VarTD |
| plot_heatmap | Plot Taxonomic Distance Heatmap |
| plot_iteration | Plot pTO Iteration Results from Run 2 or Run 3 |
| plot_radar | Radar (Spider) Chart for Multi-Community Index Comparison |
| plot_rarefaction | Plot Taxonomic Rarefaction Curve |
| plot_taxonomic_tree | Plot Taxonomic Tree as a Dendrogram |
| pto_components | Calculate All Eight pTO Components (Convenience Wrapper) |
| rarefaction_taxonomic | Taxonomic Diversity Rarefaction |
| shannon | Shannon Diversity Index |
| simpson | Simpson Diversity Index |
| simulate_td | Simulate Expected AvTD/VarTD Under Random Sampling |
| tax_distance_matrix | Compute Taxonomic Distance Matrix |
| vartd | Variation in Taxonomic Distinctness (Lambda+) |