BIEN SDM Data export and validation

Overview

The scripts in this repository export odata from the BIEN database for species distribution modeling.

For creation of the BIEN ranges database and import of complete SDM output, see: https://github.com/EnquistLab/bien-range

Application directory structure

ranges/
|__ data/ [range model data exported to here]
|   |__ rm_data_20230418/
|   |__ range_model_species_attributes.csv [list of spp & attributes]
|        |__ species/ [individual species data, one file per species]
|            |__ Aa_achalensis.csv
|            |__ Aa_peruviana.csv
|            |__ [etc.]
|__ docs/ [Miscellaneous documentation here]
|__ src/ [Application code here & git repo]
    |__ params_20230418.sh [parameters file; suffix uniquely identifies run]
    |__ range_model_data.sh [Range model data export main script]
    |__ README.md
    |__ sql/ [SQL scripts sourced by main scripts in src/]
    |   |__ multistatus_species.sql
    |   |__ range_model_data_raw.sql
    |   |__ range_model_species.sql
    |   |__ README.md
    |__ validations/ [standalone validation scripts]

Usage

All tasks are performed by main shell scripts in base directory (this one). SQL is either executed directly in main script, or sourced as SQL files in subdirectory sql/.

Export SDM species occurrence input data from BIEN analytical database

• Main script ranges/src/range_model_data.sh, call all others.
• Before running:
  • Set correct name of parameters script (e.g., "source "params_20230418.sh"

./range_model_data.sh [-m]

Notes:

• Uses parameters in params.sh. Check all carefully!
• Note especially $run: uniquely identifies the dataset used for a unique model run. Recommended format yyyymmdd; may also include additional suffix.
• After extracting data for final production run of range models, commit & tag all code and push to GitHub

[minor] Import SDM species to BIEN analytical database

• A one-time operation to import list of species to the BIEN database and add additional species traits. Unlikely to be used again.

./load_sdm_species.sh