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

Modeling variables sources

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