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