Changes in version 0.1.0 (2026-04-01)                  

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
  - Ozkan & Mert (2022) reinforced estimators:
  - 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
  - Verified against Ozkan & Mert (2022) reinforced estimator
    methodology
  - Cross-validated with Kursad Ozkan's Excel macro (TD_OMD.xlsm)
  - Documented Excel macro bug: Application.Calculate missing inside
    tekerur2() and tekerur3() loops