TerraDactyl v1.0 software archive
Description
TerraDactyl allows for the extraction of map layer data, currently curated by Google Earth Engine (GEE), at a set of point in space and time. It has been developed in tandem with eDNAExplorer.org as a means of automatically associated biodiversity data, derived from environmental DNA, with environmental conditions associated with each sample. However, these extracted environmental data can be associated with other types of data collected, not just biodiversity measurements. Quick overview of this archive: 1. Example input file for TerraDactyl: TerraDactyl_ExampleInput.csv 2. Example output file from TerraDactyl: TerraDactyl_ExampleOutput.csv 3. Overview of environmental data sets utilized by TerraDactyl: TerraDactyl_Metadata.xlsx 4. Python requirements: requirements.txt 5. Script for processing environmental maps in raster format: RasterDataset.py 6. Script for processing environmental maps in vector format: VectorDataset.py 7. The TerraDactly script: terradactyl.py 8. Shell script for running terradactyl.py in parallel over input rows of metadata (These describe sample locations and dates).
Files
Steps to reproduce
Setup 1. Install requirements: pip install -r requirements.txt 2. Install parallel: sudo apt install parallel Note: You will need to pass the GEE Credentials as parameters or change the variable at the top of terradactyl.sh Workflow 1. Provide an input CSV file containing the following information for each sample. An example input file is TerraDactyl_ExampleInput.csv. The input file headers are: Longitude/Latitude: In decimal degrees north and east (Using the EPSG:4326 coordinate reference system). Sample Date: The date associated with each sample. The default format is YYYY-MM-DD. Sample ID: A unique identifier string for each sample. Spatial Uncertainty: The uncertainty in position, in meters, associated with each point. If no value is provided, or if the uncertainty provided is under 30 meters, then a default value of 30 meters will be assigned. 2. Run terradactyl.sh: ./terradactyl.sh 3. Collect output file containing extracted environmental values associated with each sample location and date. An example output file from TerraDactyl: TerraDactyl_ExampleOutput.csv A description of the environmental data sets utilized by TerraDactyl: TerraDactyl_Metadata.xlsx