Package index • taxdiv

Quick Start

Start here. These two functions handle multi-site batch processing and multi-community comparison — the fastest way to get results from your data.

batch_analysis(): Batch Analysis from a Single Data Frame
compare_indices(): Compare All Diversity Indices Side by Side

Classical Diversity Indices

Shannon-Wiener (H’) and Gini-Simpson indices — the most widely used diversity measures in ecology. Shannon includes three bias correction methods: Miller-Madow, Grassberger, and Chao-Shen.

shannon(): Shannon Diversity Index
simpson(): Simpson Diversity Index

Clarke & Warwick Taxonomic Distinctness

Path-length-based taxonomic distinctness measures. Delta and Delta* are abundance-weighted; AvTD and VarTD are presence/absence-based and sample-size independent.

delta(): Taxonomic Diversity Index (Delta)
delta_star(): Taxonomic Distinctness (Delta*)
avtd(): Average Taxonomic Distinctness (Delta+)
vartd(): Variation in Taxonomic Distinctness (Lambda+)

Ozkan pTO — Core Functions

Deng entropy-based taxonomic diversity following Ozkan (2018). Produces 8 complementary indices (uTO, TO, uTO+, TO+ and their max-informative-level variants).

ozkan_pto(): Calculate Ozkan's Taxonomic Diversity Index (pTO)
pto_components(): Calculate All Eight pTO Components (Convenience Wrapper)
deng_entropy_level(): Calculate Deng Entropy at a Single Taxonomic Level

Ozkan pTO — Full Pipeline

The complete three-run pipeline: deterministic calculation (Run 1), stochastic resampling with slicing (Run 2), max-informative levels (Run 3), plus jackknife and sensitivity analysis.

ozkan_pto_full(): Full Ozkan pTO Pipeline (Islem 1 + 2 + 3)
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)
ozkan_pto_jackknife(): Jackknife Analysis for Ozkan's pTO Index (Islem 1 / Run 1)

Simulation & Significance Testing

Random subsampling from a master species pool to generate expected distributions of AvTD and VarTD. Use with plot_funnel() for 95% confidence funnels and statistical significance testing.

simulate_td(): Simulate Expected AvTD/VarTD Under Random Sampling
rarefaction_taxonomic(): Taxonomic Diversity Rarefaction

Visualization

Seven ggplot2-based plot types covering significance testing, rarefaction, resampling trajectories, community comparison, similarity patterns, composition, and taxonomic structure.

plot_funnel(): Funnel Plot for AvTD/VarTD
plot_rarefaction(): Plot Taxonomic Rarefaction Curve
plot_iteration(): Plot pTO Iteration Results from Run 2 or Run 3
plot_radar(): Radar (Spider) Chart for Multi-Community Index Comparison
plot_heatmap(): Plot Taxonomic Distance Heatmap
plot_bubble(): Bubble Chart of Species Contributions to Diversity
plot_taxonomic_tree(): Plot Taxonomic Tree as a Dendrogram

Taxonomic Tree & Distance

Build taxonomic classification trees from species-level data and compute pairwise taxonomic distance matrices used by Clarke & Warwick and Ozkan pTO methods.

build_tax_tree(): Build a Taxonomic Tree from Species Data
tax_distance_matrix(): Compute Taxonomic Distance Matrix

Example Datasets

Ready-to-use ecological community datasets from Mediterranean forest ecosystems in Anatolia, Turkey. Includes abundance data and full taxonomic classifications.

anatolian_trees: Anatolian Forest Trees: Multi-Site Species Data
gazi_comm: Example Community Vector: 8 Anatolian Tree Species
gazi_gytk: Example Taxonomy: 8 Anatolian Tree Species