From Raw Data to Publication-Ready Results | Step 1: Prepare Your Data | Single community (named vector) | Taxonomic tree | Multiple sites (data frame) | Step 2: Compute All Indices at Once | Single community --- compare_indices() | Multiple sites --- batch_analysis() | Step 3: Run the Full Ozkan Pipeline | Step 4: Visualize Results | Compare communities side by side | Inspect the taxonomic tree | Rarefaction curve | Step 5: Export Results | Save to CSV | Save to Excel | Quick Reference: Which Function to Use?
Package: taxdiv 1.0.0
taxdiv: Taxonomic Diversity Indices Using Deng Entropy
Calculates taxonomic diversity indices for ecological community data using Deng entropy framework and classical approaches (Shannon, Simpson, Clarke & Warwick). Provides functions for computing taxonomic distinctness, average taxonomic distinctness (AvTD/Delta+), variation in taxonomic distinctness (VarTD/Lambda+), and Deng entropy-based measures that incorporate taxonomic hierarchy information. Includes tools for constructing taxonomic trees and computing pairwise taxonomic distances. Methods are described in Ozkan (2018) <doi:10.18182/tjf.441061>, Clarke & Warwick (1998) <doi:10.1046/j.1365-2664.1998.3540523.x>, Ozkan & Mert (2022) <doi:10.5152/forestist.2021.21025>, Shannon (1948) <doi:10.1002/j.1538-7305.1948.tb01338.x>, and Simpson (1949) <doi:10.1038/163688a0>.
Authors:
taxdiv_1.0.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
taxdiv/json (API)
| # Install 'taxdiv' in R: |
| install.packages('taxdiv', repos = c('https://mgorgoz.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mgorgoz/taxonomic-diversity-r/issues
Pkgdown/docs site:https://mgorgoz.github.io
Datasets:
- 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
Last updated from:006580f6d0. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 150 | ||
| source / vignettes | OK | 246 | ||
| linux-release-x86_64 | OK | 220 | ||
| macos-release-arm64 | OK | 139 | ||
| macos-oldrel-arm64 | OK | 147 | ||
| windows-devel | OK | 157 | ||
| windows-release | OK | 130 | ||
| windows-oldrel | OK | 127 | ||
| wasm-release | OK | 111 |
Exports:avtdbatch_analysisbuild_tax_treecompare_indicesdeltadelta_stardeng_entropy_levelozkan_ptoozkan_pto_fullozkan_pto_jackknifeozkan_pto_resampleozkan_pto_sensitivityplot_bubbleplot_funnelplot_heatmapplot_iterationplot_radarplot_rarefactionplot_taxonomic_treepto_componentsrarefaction_taxonomicshannonsimpsonsimulate_tdtax_distance_matrixtaxdiv_explorervartd
Dependencies:rlang
Complete Workflow: From Data to Results
Last update: 2026-06-09
Started: 2026-03-28
Introduction to taxdiv
Overview | Example Data: Mediterranean Forest Community | Classical Diversity Indices | Taxonomic Distance | Clarke & Warwick Taxonomic Distinctness | Deng Entropy and Ozkan pTO | Convenience wrapper | Comparing Communities | Stochastic Resampling (Run 2) | Sensitivity Analysis (Run 3) | Species Inclusion Probabilities | Full Pipeline Summary | Rarefaction | Visualization | Taxonomic Tree (Dendrogram) | Taxonomic Distance Heatmap | Community Comparison (Bar Plot) | Iteration Plot (Run 2) | Bubble Chart | Radar Chart (Spider Plot) | Rarefaction Curve | References
Last update: 2026-06-09
Started: 2026-02-15
Ozkan pTO Method: Deng Entropy-Based Taxonomic Diversity
What Is the Ozkan pTO Method? | From Shannon to Deng: Why a New Entropy? | Deng Entropy at Each Taxonomic Level | The 8 Indices Explained | Weighted vs Unweighted | With vs Without Species-Level Shannon | All Levels vs Max-Informative Levels | Which index to use? | The Three-Run Pipeline | Run 1: Deterministic Calculation | Run 2: Stochastic Resampling (Slicing) | Visualizing Run 2 | Run 3: Max-Informative Level Variants | Full Pipeline in One Call | Jackknife Leave-One-Out Analysis | Comparing Communities | References
Last update: 2026-06-09
Started: 2026-03-28
taxdiv Paketi Kullanim Rehberi (Turkce)
Bu Paket Ne Ise Yarar? | Ornek Veri: Akdeniz Ormani Toplulugu | Adim 1: Klasik Cesitlilik Indeksleri | Adim 2: Taksonomik Mesafe Matrisi | Adim 3: Clarke & Warwick Taksonomik Ayirt Edicilik | Adim 4: Deng Entropisi ve Ozkan pTO (Islem 1) | max_level parametresi | 8 Bilesenli Cikti | Adim 5: Stokastik Yeniden Ornekleme (Islem 2 / Run 2) | Adim 6: Duyarlilik Analizi (Islem 3 / Run 3) | Tur Dahil Etme Olasiliklari | Adim 7: Tam Pipeline (ozkan_pto_full) | Adim 8: Jackknife Yanliliksiz Tahmin | Adim 9: Toplu Analiz (batch_analysis) | Adim 10: Rarefaction (Seyreltme) | Adim 11: Simuelasyon ve Huni Grafigi (Funnel Plot) | Gorsellestime | Taksonomik Agac (Dendogram) | Taksonomik Mesafe Isi Haritasi (Heatmap) | Indeks Karsilastirma (Bar Plot) | Islem 2 Iterasyon Grafigi | Tur Katki Baloncuk Grafigi (Bubble Chart) | Radar Grafigi (Spider Chart) | Seyreltme Egrisi (Rarefaction Curve) | Huni Grafigi (Funnel Plot) | Matematiksel Arka Plan | Shannon Entropisi | Simpson Indeksi | Clarke & Warwick: Taksonomik Ayirt Edicilik | Deng Entropisi | Ozkan pTO Formulu | Adim Adim Hesaplama Ornegi | Veri | Adim 1: Shannon | Adim 2: Taksonomik Mesafe | Adim 3: AvTD (Elle) | Adim 4: Deng Entropisi (Tur Seviyesinde) | Adim 5: Ozkan pTO | Fonksiyon Listesi | Klasik Indeksler | Clarke & Warwick Taksonomik Ayirt Edicilik | Ozkan pTO (Deng Entropisi) | Ozkan pTO Pipeline | Toplu Analiz ve Karsilastirma | Simulasyon ve Rarefaction | Gorsellestime (7 plot tipi) | Yardimci Fonksiyonlar | Veri Setleri | Kaynaklar | Klasik Cesitlilik Indeksleri | Taksonomik Farklilik | Deng Entropisi ve Kanit Teorisi | Ozkan pTO Indeksi | Yanliliksiz Tahmin | Rarefaction (Seyreltme)
Last update: 2026-06-09
Started: 2026-02-22
Visualization Guide
Overview | Quick Reference | 1. Taxonomic Tree (Dendrogram) | 2. Taxonomic Distance Heatmap | 3. Bubble Chart | 4. Radar Chart (Spider Plot) | 5. Iteration Plot (Run 2) | 6. Rarefaction Curve | 7. Funnel Plot | Customizing Plots
Last update: 2026-06-09
Started: 2026-03-28
Clarke & Warwick Taxonomic Distinctness
What Is Taxonomic Distinctness? | The Taxonomic Distance Matrix | The Four Indices | Delta --- Taxonomic Diversity | Delta* --- Taxonomic Distinctness (abundance-weighted) | AvTD (Delta+) --- Average Taxonomic Distinctness | VarTD (Lambda+) --- Variation in Taxonomic Distinctness | Comparing the Four Indices | Significance Testing with Funnel Plots | Running the simulation | Funnel plot | When to Use Clarke & Warwick vs Ozkan pTO | References
Last update: 2026-03-28
Started: 2026-03-28
Classical Diversity Indices: Shannon and Simpson
What Are Classical Diversity Indices? | Shannon-Wiener Index (H') | The idea | The formula | Key properties | Usage in taxdiv | Bias Correction | Simpson Index | Three variants | Understanding the variants | Shannon vs Simpson: When to Use Which? | The Limitation: Why You Need Taxonomic Indices Too | References
Last update: 2026-03-28
Started: 2026-03-28
