taxdiv 0.1.0

Initial release of taxdiv — taxonomic diversity indices using Deng entropy.

Core Functions

• Deng entropy at any taxonomic level (deng_entropy_level())
• Ozkan (2018) pTO with slicing procedure (ozkan_pto(), pto_components())
  • 8 indices: uTO, TO, uTO+, TO+, uTO_max, TO_max, uTO+_max, TO+_max
  • max_level parameter for controlling taxonomic depth (NULL, “auto”, integer)
  • Presence-based entropy: equal weight (1/S) at each slice
• Stochastic resampling — Run 2 (ozkan_pto_resample())
  • Random species inclusion/exclusion (50% probability per species)
  • Configurable iteration count and seed for reproducibility
• Sensitivity analysis — Run 3 (ozkan_pto_sensitivity())
  • Species-specific inclusion probabilities derived from Run 2
  • Overall maximum across Run 1 + 2 + 3
• Jackknife leave-one-out analysis (ozkan_pto_jackknife())
• Full pipeline in one call (ozkan_pto_full())
  • Combines Run 1 + Run 2 + Run 3 + jackknife
• Classical indices: Shannon H’ (shannon()) and Gini-Simpson (simpson())
  • Bias correction methods: Miller-Madow, Grassberger, Chao-Shen
• Clarke & Warwick taxonomic distinctness:
  • Taxonomic diversity Delta (delta())
  • Taxonomic distinctness Delta* (delta_star())
  • Average taxonomic distinctness AvTD/Delta+ (avtd())
  • Variation in taxonomic distinctness VarTD/Lambda+ (vartd())
• Multi-community comparison (compare_indices()) — 14 indices side by side
• Multi-site batch analysis (batch_analysis()) — automatic column detection
• Simulation-based significance testing (simulate_td())
  • Random subsampling from species pool for AvTD/VarTD confidence funnels
• Taxonomic rarefaction with bootstrap CI (rarefaction_taxonomic())
  • 8 index choices, configurable sample sizes and iterations
• Taxonomic distance matrix (tax_distance_matrix())
• Taxonomy tree builder (build_tax_tree())
• Parallel computing support for simulate_td(), rarefaction_taxonomic(), and batch_analysis() via parallel and n_cores parameters

S3 Class System

• 6 S3 classes: compare_indices, batch_analysis, ozkan_pto, ozkan_pto_resample, ozkan_pto_sensitivity, rarefaction_taxonomic, td_simulation
• 13 S3 methods: print(), summary(), and plot() for all main outputs

Visualization

• Funnel plot for AvTD/VarTD significance testing (plot_funnel())
• Rarefaction curves with bootstrap CI (plot_rarefaction())
• Stochastic resampling iteration trajectories (plot_iteration())
• Radar/spider chart for multi-community comparison (plot_radar())
• Taxonomic similarity heatmap (plot_heatmap())
• Bubble plot of community composition (plot_bubble())
• Dendrogram of taxonomic hierarchy (plot_taxonomic_tree())

Example Datasets

• anatolian_trees — Anatolian tree species with full taxonomic hierarchy
• gazi_comm — Community abundance data from Gazi University campus
• gazi_gytk — Taxonomic classification for Gazi campus species

Documentation

• English vignette with 7 plots and worked examples
• Turkish (Turkce) vignette with 8 plots, formulas, and full walkthrough
• pkgdown website: https://mgorgoz.github.io/taxonomic-diversity-r/
• Pseudocode for pTO Run 1/2/3 (inst/pseudocode/taxonomic_diversity_pseudocode.md)
• Pseudocode for Clarke & Warwick (inst/pseudocode/taxonomic_distance_pseudocode.md)

Testing

• 610 assertions across 12 test files
• Integration tests covering full Run 1 -> 2 -> 3 pipeline
• Reproducibility tests with seed control
• Mathematical relationship checks (ordering constraints, boundary cases)
• R CMD check: 0 errors, 0 warnings, 0 notes

Validation

• Verified against Ozkan (2018) hypothetical examples
• Cross-validated with Kursad Ozkan’s Excel macro (TD_OMD.xlsm)
• Documented Excel macro bug: Application.Calculate missing inside tekerur2() and tekerur3() loops