environment

Introduction

environment is a sub-project of the BioForest project aimed at gathering environmental variables of climate (TerraClimate), soil (SoilGrids) and landscape (TMF) for data preparation within the project.

Usage

environment takes advantage of snakemake and conda for data retrieval defined by the sites list. First check the sites list in config/sites.tsv and you can run the whole workflow with snakemake -j #cores –use-conda –keep-going . Further details on usage can be found in https://bioforest-project.github.io/environment/10_methods.html . Then all analyses rely on the quarto documents (files.qmd) that can be run with R and associated environment defined with renv.

Project

environment includes:

• snakemake and conda workflow for automatic data retrieval:
  • Workflow definition in Snakefile
  • Worflow scripts in scripts/
  • Workflow configuration in config/
  • conda environments in envs/
• 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/
• 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 environment: https://github.com/Bioforest-project/environment/issues . You may however reach us by mail with people from the core group (see below).

Core group

• Sylvain Schmitt (sylvain.schmitt@cirad.fr)
• Camille Piponiot-Laroche (camille.piponiot-laroche@cirad.fr)
• Géraldine Derroire (geraldine.derroire@cirad.fr)
• Mithila Unkule (mithila.unkule@fondationbiodiversite.fr)
• Irié Cazimir Zo-Bi (iczobi@gmail.com)
• Anand Roopsind (aroopsind@gmail.com)

The whole group consist of participants to the Bioforest project.