geoenrich 0.5.8 documentation

GeoEnrich provides functionalities to enrich georeferenced events (such as species occurrences) with environmental data from satellites or models. Users can specify a geographic or temporal buffer to include data in the neighbourhood of occurrences into their analyses. Two main outputs are available: a simple summary of the variable in the requested area, or the full data (as a geotiff raster, a png image, or a numpy array).

Sea surface temperature, chlorophyll, and 40 other environmental variables are available natively, and others can easily be added by the user. This package is intended for large numbers of occurrences: local storage is implemented to avoid redundant requests to remote servers.

The package provides functions to retrieve occurrence data directly from GBIF, or open a custom dataset from any source. Arbitrary areas defined by the user can also be enriched.

Source on GitHub at morand-g/geoenrich

Illustration of an occurrence dataset enriched with bathymetry data

This project is being developed as part of the G2OI project, cofinanced by the European union, the Reunion region, and the French Republic.

How to cite

As this package is distributed under a GPLv3 license, you have no obligation to cite the authors when you use it. If you want to cite the package to ensure reproducibility, please consider doing it the following way:

Gaetan Morand. (2022). GeoEnrich v0.X: a new tool for scientists to painlessly enrich species occurrence data with environmental variables (v0.X). Zenodo. DOI:10.5281/zenodo.6458090

You can find the specific DOI for the version you are using on the package’s Zenodo page.

Installation

• Installation instructions for Python
  • 1. Work environment
  • 2. Prerequisites
  • 3. Installation
  • 4. Configuration
    • 4.1. First configuration
    • 4.2. Adding other data sources
  • 6. Using the package
• Installation instructions for R
  • 1. Prerequisites
  • 2. Installation
  • 3. Configuration
    • 3.1. First configuration
    • 3.2. Adding other data sources
  • 4. Using the package

Usage

• Tutorial for Python users
  • Load your occurrence data
    • If you are using your own dataset (DarwinCore format)
    • If you are using your own dataset (csv format)
    • If you do not have occurrences but want to enrich arbitrary areas
    • Create enrichment file
  • Enrich
    • Define enrichment scope
    • Only enrich a small slice first to check speed.
    • For large areas, use downsample argument to download only part of available data (to reduce download time)
  • Data retrieval
    • Check the enrichment status of the dataset.
    • Export summary statistics to a csv file
    • Export data as a raster layer for the first occurrence of the dataset
    • Export data as a png file for the first occurrence of the dataset
    • Retrieve the raw data and plot it
  • Using occurrence data from GBIF
    • Get GBIF id for the taxon of interest
    • Request an archive with all occurrences of this taxon
    • Download request
    • You can then load data using open_dwca and the taxon_key parameter
• Tutorial for R users
  • Load your occurrence data
    • If you are using your own dataset (DarwinCore format)
    • If you are using your own dataset (csv format)
    • If you do not have occurrences but want to enrich arbitrary areas
    • Create enrichment file
  • Enrich
    • Define enrichment scope
    • Only enrich a small slice first to check speed.
    • For large areas, use downsample argument to download only part of available data (to reduce download time)
  • Data retrieval
    • Check the enrichment status of the dataset.
    • Export summary statistics to a csv file
    • Export data as a raster layer for the first occurrence of the dataset
    • Export data as a png file for the first occurrence of the dataset
    • Retrieve the raw data and plot it
• Examples of input data
  • 1. Enriching occurrences
    • 1.1. DarwinCore archive
    • 1.2. CSV file
  • 2. Enriching areas
• Available variables

Online version

• Geoenrich online (beta)
  • 1. File format
    • 1.1. Species occurrences
    • 1.2. Areas
  • 2. Restrictions
  • 3. Setting up the self-hosted version

Modules

Dataloader module

The dataloader module: import DarwinCore archives, download data from GBIF.

Enrichment module

The enrichment module: download enrichment data, handle enrichment files.

Exports module

The exports module: retrieve downloaded data, calculate statistics, export data to pictures.

Satellite module

The satellite module (internal use): netCDF file handling, data download, data retrieval.

Indices and tables

• Index

• Search Page