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SAGHAS - Database

💻 What is it ?

Sowing AGrobiodiversity to HArvest Sustainability

Context :

At +2°C, up to 50% crop losses can be expected.

Building new crop combinaison on biodiversity is a promising option.

Identifying the best plant combinaitions to suit agronomic, climatic, cultural and societal contexts remains a challange.

Aim of this repository : Build a database of cultivated plants that can be analysed as part of ongoing projects into the sustainability of agriculture and food safety.

🔍 Repository description

├── data
│   ├── 🔨 additional_data
│   ├── 🔨 intermediate_data
│   ├── output_data
│   └── raw_data
├── README.md
├── SAGHAS.Rproj
└── src
    ├── 10-cleanning_raw_data
    ├── 11-standardize_species_names_of_external_DB
    ├── 20-merging_raw_data
    ├── 30-origin_areas
    ├── 40-usages
    ├── 50-traits_integration
    ├── 90-shiny_app
    └── functions

🔨 -> Directory created by R script

partner.sh is used to download necessary data that is not in this repository, but it must be updated

The src directory contains all R script files (essentially Quarto files for the moment) organized in different directories:

  • 10-cleanning-raw-data : For each source, a script was written to structure data and correct some typos.

  • 11-standardize_species names_of_external_DB : Contains one R script that standardizes species names from TRY and GRIN with WCVP. In order to make those data easier to use. It takes a lot of time (~15h).

  • 20-merging_raw_data : Merge all species lists and standardise scienctific names with WCVP.

  • 30-origin_areas : Structure native and introduced areas from WCVP into two tables. And structure primary regions of diversity from FAO. Those tables follow the lower level of the standard WGSRPD.

  • 40-usages : Structure usages from GRIN and FAO data into two tables. Merge those usages in a third table

  • 50-traits_integration : Will integrate to the SAGHAS database, traits values from TRY database. It is under development and not currently usable

  • 90-shiny_app

💾 Structure of the ouput data

🏗️ Status

under development

🛠️ Support

email : martin.davy@ird.fr

🙏 Authors and acknowledgment