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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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.