# Taxonomic Diversity Indices Using Deng Entropy

## Documentation for package ‘taxdiv’ version 0.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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+)