Package: taxdiv 0.1.0

Muhammet Murat Gorgoz

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.

Authors:Muhammet Murat Gorgoz [aut, cre], Kursad Ozkan [aut], Mehmet Guvenc Negiz [aut]

taxdiv_0.1.0.tar.gz
taxdiv_0.1.0.tar.gz(r-4.7-any)taxdiv_0.1.0.tar.gz(r-4.6-any)
taxdiv_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
taxdiv/json (API)
NEWS

# Install 'taxdiv' in R:
install.packages('taxdiv', repos = c('https://cran.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

On CRAN:

Conda:

3.54 score 461 downloads 26 exports 1 dependencies

Last updated from:231aad7c2b. Checks:4 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK166
source / vignettesOK212
linux-release-x86_64OK136
wasm-releaseOK108

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_matrixvartd

Dependencies:rlang

Clarke & Warwick Taxonomic Distinctness

Rendered fromclarke-warwick.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2026-04-01
Started: 2026-04-01

Classical Diversity Indices: Shannon and Simpson

Rendered fromclassical-indices.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2026-04-01
Started: 2026-04-01

Complete Workflow: From Data to Results

Rendered fromworkflow.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2026-04-01
Started: 2026-04-01

Introduction to taxdiv

Rendered fromintroduction.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2026-04-01
Started: 2026-04-01

Ozkan pTO Method: Deng Entropy-Based Taxonomic Diversity

Rendered fromozkan-pto.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2026-04-01
Started: 2026-04-01

taxdiv Paketi Kullanim Rehberi (Turkce)

Rendered fromgiris_rehberi.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2026-04-01
Started: 2026-04-01

Visualization Guide

Rendered fromvisualization.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2026-04-01
Started: 2026-04-01

Readme and manuals

Help Manual

Help pageTopics
Anatolian Forest Trees: Multi-Site Species Dataanatolian_trees
Average Taxonomic Distinctness (Delta+)avtd
Batch Analysis from a Single Data Framebatch_analysis
Build a Taxonomic Tree from Species Databuild_tax_tree
Compare All Diversity Indices Side by Sidecompare_indices
Taxonomic Diversity Index (Delta)delta
Taxonomic Distinctness (Delta*)delta_star
Calculate Deng Entropy at a Single Taxonomic Leveldeng_entropy_level
Example Community Vector: 8 Anatolian Tree Speciesgazi_comm
Example Taxonomy: 8 Anatolian Tree Speciesgazi_gytk
Calculate Ozkan's Taxonomic Diversity Index (pTO)ozkan_pto
Full Ozkan pTO Pipeline (Islem 1 + 2 + 3)ozkan_pto_full
Jackknife Analysis for Ozkan's pTO Index (Islem 1 / Run 1)ozkan_pto_jackknife
Stochastic Resampling of Ozkan's pTO Index (Islem 2 / Run 2)ozkan_pto_resample
Sensitivity Analysis of Ozkan's pTO Index (Islem 3 / Run 3)ozkan_pto_sensitivity
Bubble Chart of Species Contributions to Diversityplot_bubble
Funnel Plot for AvTD/VarTDplot_funnel
Plot Taxonomic Distance Heatmapplot_heatmap
Plot pTO Iteration Results from Run 2 or Run 3plot_iteration
Radar (Spider) Chart for Multi-Community Index Comparisonplot_radar
Plot Taxonomic Rarefaction Curveplot_rarefaction
Plot Taxonomic Tree as a Dendrogramplot_taxonomic_tree
Calculate All Eight pTO Components (Convenience Wrapper)pto_components
Taxonomic Diversity Rarefactionrarefaction_taxonomic
Shannon Diversity Indexshannon
Simpson Diversity Indexsimpson
Simulate Expected AvTD/VarTD Under Random Samplingsimulate_td
Compute Taxonomic Distance Matrixtax_distance_matrix
Variation in Taxonomic Distinctness (Lambda+)vartd