An indicator of the conservation status of useful wild plants

Project Management and method code for "Comprehensiveness of conservation of useful wild plants: an operational indicator for biodiversity and sustainable development targets"

Khoury CK, Amariles D, Soto JS, Diaz MV, Sotelo S, Sosa CC, Ramírez-Villegas J, Achicanoy HA, Velásquez-Tibatá J, Guarino L, León B, Navarro-Racines C, Castañeda-Álvarez NP, Dempewolf H, Wiersema JH, and Andy Jarvis (2018). Comprehensiveness of conservation of useful wild plants: an operational indicator for biodiversity and sustainable development targets. Ecological Indicators 98: 420-429. doi: 10.1016/j.ecolind.2018.11.016. https://doi.org/10.1016/j.ecolind.2018.11.016

Khoury CK, Amariles D, Soto JS, Diaz MV, Sotelo S, Sosa CC, Ramírez-Villegas J, Achicanoy HA, León B, and JH Wiersema (2018). Data for the calculation of an indicator of the comprehensiveness of conservation of useful wild plants. Data in Brief 22: 90-97. doi: 10.1016/j.dib.2018.11.125. https://doi.org/10.1016/j.dib.2018.11.125

Funding: Research at the International Center for Tropical Agriculture was funded by the Biodiversity Indicators Partnership, an initiative supported by UN Environment, the European Commission and the Swiss Federal Office for the Environment. The funder played no role in study design; in the collection, analysis and interpretation of data; in the writing of the report; or in the decision to submit the article for publication.

Project Website https://ciat.cgiar.org/usefulplants-indicator/.

Functions documentation standard

# Function description
# @param (type) parameter description
# @return (type) result description

File names standard

• lower case
• no spaces, only underlines

File structure

src/
├── 0_cleaning/
├── 1_modeling/
│   ├── 1_1_maxent/
|   │   ├── calibration
|   │   ├── run
|   │   └── evaluation
│   └── 1_2_alternatives
|       ├── ca50
|       ├── gdm
|       └── convexhull
├── 2_gap_analysis/
│   ├── ex_situ/
|   │   ├── ca50_g
|   │   ├── srs
|   │   ├── grs
|   │   ├── ers
|   │   └── fcs
│   └── in_situ/
|       ├── grs
|       ├── ers
|       └── fcs
└── 3_indicator/

Git branching

• master: only for releases, don't touch!
• develop: current development, changes to share with the team
• issue##: your current resolving issue, document first the issue

Data files

Folder	File	Description
WEP	WEP.csv	World Economic Plants database (USDA ARS GRIN-GLOBAL Taxonomy https://npgsweb.ars-grin.gov/gringlobal/taxon/taxonomysearcheco.aspx)
GBIF	gbif.zip	GBIF download of Plantae from 1950 to date (https://www.gbif.org/)
GENESYS	genesys_zip	GENESYS Original occurrence records from genebanks (genebank accession records) https://www.genesys-pgr.org/welcome
CWR	cwr.zip	Crop Wild Relatives database of Global CWR Project (https://www.cwrdiversity.org/checklist/cwr-occurrences.php)
COUNTRY	countryISO.csv	Country names, ISO 3166-1 alpha-3 and alpha-2

Modeling variables sources

Variable	Name	Source
elevation	SRTM 90m Digital Elevation Data	CGIAR
bioclimatic variables	WorldClim Version2	WordlClim
solar radiation	WorldClim Version2	WordlClim
wind speed	WorldClim Version2	WordlClim
water vapor pressure	WorldClim Version2	WordlClim

Modeling parameters

Principal modeling: maxent2

Alternative modeling: CA50

Resolution: 2.5 arc minutes

K=5 mean as final evaluation

Modeling evaluation

AUC mean >= 0.7

SDAUC < 0.15

ASD15 <= 10%

CAUC >= 0.4