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/
- Workflow definition in
- Analyse of the data with associated documentation and figures:
- Reproductive analyses in
files.qmd
- Resulting pages in
docs/
- Document structure definition in
_quarto.yml
- Reproductive analyses in
- Data in
data/
with:- All raw data in
raw_data/
- All derived data in
derived_sata/
- All raw data in
- Intermediary files in
outputs/
- Figures in
figures/
- R environment definition with renv in
renv/
andrenv/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.