Diversity

Published

June 25, 2025

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Introduction

LoggingDiversity is a sub-project of the BioForest project aimed at studying the Interactions between tree biodiversity, forest dynamics and climate in managed tropical forests with a pan-tropical approach. Specifically, LoggingDiversity focus on the effects of logging disturbance on tropical forest diversity - a global assessment with the following question: What is the effect of logging intensity on biodiversity, and how does it change through time?

Usage

All diversity analyses rely on the quarto documents (files.qmd) that can be run with R and associated environment defined with renv.

Project

species includes:

  • Analyse of the data with associated documentation and figures:
    • Reproductive analyses in files.qmd
    • Resulting pages in docs/
    • Document structure definition in _quarto.yml
  • Data in data/ with:

    • All raw data in raw_data/

    • All derived data in derived_sata/

  • Intermediary files in outputs/
  • Figures in figures/
  • Models in models/
  • R environment definition with renv in renv/ and renv/lock
  • R files (.Rbuildignore , .Rdata , .Rprofile , .Rhistory)
  • Git and GitHub files (.gitignore , .github/)
  • Project documentation (README.qmd , README.md , NEWS.md, LICENSE )

Contribution

You can contribute to the project by forking the repository on github and cloning the fork to your machine using several options, including GitHub desktop GUI. Further informations on contribution are detailed in the online document: https://bioforest-project.github.io/data_preparation/98_contributing.html.

Help

Please preferentially create an issue on GitHub for any questions, bugs or help needed regarding diversity: https://github.com/Bioforest-project/LoggingDiversity/issues . You may however reach us by mail with people from the core group (see below).

Core group

  • Sylvain Schmitt (sylvain.schmitt@cirad.fr)
  • Genoveva Gatti (genogatti@gmail.com)
  • David Burslem (d.burslem@abdn.ac.uk)
  • Andes Hamuraby Rozak (andes.hamuraby.rozak@brin.go.id)
  • Natalia Bedrij (nabedrij@gmail.com)
  • Verginia Wortel (wortelv@gmail.com)

The whole group consist of participants to the Bioforest project.