https://github.com/earth-chris/elapid
Species distribution modeling tools, including a python implementation of Maxent
https://github.com/earth-chris/elapid
biodiversity-informatics biogeography geospatial maxent niche-modelling species-distribution-modelling
Last synced: 5 months ago
JSON representation
Species distribution modeling tools, including a python implementation of Maxent
- Host: GitHub
- URL: https://github.com/earth-chris/elapid
- Owner: earth-chris
- License: mit
- Created: 2021-03-20T04:00:24.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2024-08-09T06:59:02.000Z (8 months ago)
- Last Synced: 2024-10-29T16:17:31.970Z (6 months ago)
- Topics: biodiversity-informatics, biogeography, geospatial, maxent, niche-modelling, species-distribution-modelling
- Language: Python
- Homepage: https://elapid.org
- Size: 6.62 MB
- Stars: 52
- Watchers: 7
- Forks: 7
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Contributing: docs/contributing.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
- open-sustainable-technology - elapid - Species distribution modeling tools, including a python implementation of Maxent. (Biosphere / Species Distribution Modeling)
README
Contemporary species distribution modeling tools for python.
[](https://doi.org/10.21105/joss.04930)
---
**Documentation**: [earth-chris.github.io/elapid](https://earth-chris.github.io/elapid)
**Source code**: [earth-chris/elapid](https://github.com/earth-chris/elapid)
---
## :snake: Introduction
`elapid` is a series of species distribution modeling tools for python. This includes a custom implementation of [Maxent][home-maxent] and a suite of methods to simplify working with biogeography data.
The name is an homage to *A Biogeographic Analysis of Australian Elapid Snakes* (H.A. Nix, 1986), the paper widely credited with defining the essential bioclimatic variables to use in species distribution modeling. It's also a snake pun (a python wrapper for mapping snake biogeography).
---
## :seedling: Installation
`pip install elapid` or `conda install -c conda-forge elapid`
Installing `glmnet` is optional, but recommended. This can be done with `pip install elapid[glmnet]` or `conda install -c conda-forge elapid glmnet`. For more support, and for information on why this package is recommended, see [this page](https://elapid.org/install#installing-glmnet).
The `conda` install is recommended for Windows users. While there is a `pip` distribution, you may experience some challenges. The easiest way to overcome them is to use [Windows Subsystem for Linux (WSL)](https://docs.microsoft.com/en-us/windows/wsl/about). Otherwise, see [this page](https://elapid.org/install) for support.
---
## :deciduous_tree: Why use elapid?
The amount and quality of bioegeographic data has increased dramatically over the past decade, as have cloud-based tools for working with it. `elapid` was designed to provide a set of modern, python-based tools for working with species occurrence records and environmental covariates to map different dimensions of a species' niche.
`elapid` supports working with modern geospatial data formats and uses contemporary approaches to training statistical models. It uses `sklearn` conventions to fit and apply models, `rasterio` to handle raster operations, `geopandas` for vector operations, and processes data under the hood with `numpy`.
This makes it easier to do things like fit/apply models to multi-temporal and multi-scale data, fit geographically-weighted models, create ensembles, precisely define background point distributions, and summarize model predictions.
It does the following things reasonably well:
:globe_with_meridians: **Point sampling**
Select random geographic point samples (aka background or pseudoabsence points) within polygons or rasters, handling `nodata` locations, as well as sampling from bias maps (using `elapid.sample_raster()`, `elapid.sample_vector()`, or `elapid.sample_bias_file()`).
:chart_with_upwards_trend: **Vector annotation**
Extract and annotate point data from rasters, creating `GeoDataFrames` with sample locations and their matching covariate values (using `elapid.annotate()`). On-the-fly reprojection, dropping nodata, multi-band inputs and multi-file inputs are all supported.
:bar_chart: **Zonal statistics**
Calculate zonal statistics from multi-band, multi-raster data into a single `GeoDataFrame` from one command (using `elapid.zonal_stats()`).
:bug: **Feature transformations**
Transform covariate data into derivative `features` to expand data dimensionality and improve prediction accuracy (like `elapid.ProductTransformer()`, `elapid.HingeTransformer()`, or the all-in-one `elapid.MaxentFeatureTransformer()`).
:bird: **Species distribution modeling**
Train and apply species distribution models based on annotated point data, configured with sensible defaults (like `elapid.MaxentModel()` and `elapid.NicheEnvelopeModel()`).
:satellite: **Training spatially-aware models**
Compute spatially-explicit sample weights, checkerboard train/test splits, or geographically-clustered cross-validation splits to reduce spatial autocorellation effects (with `elapid.distance_weights()`, `elapid.checkerboard_split()` and `elapid.GeographicKFold()`).
:earth_asia: **Applying models to rasters**
Apply any pixel-based model with a `.predict()` method to raster data to easily create prediction probability maps (like training a `RandomForestClassifier()` and applying with `elapid.apply_model_to_rasters()`).
:cloud: **Cloud-native geo support**
Work with cloud- or web-hosted raster/vector data (on `https://`, `gs://`, `s3://`, etc.) to keep your disk free of temporary files.
Check out some example code snippets and workflows on the [Working with Geospatial Data](https://elapid.org/examples/WorkingWithGeospatialData/) page.
---
:snake: `elapid` requires some effort on the user's part to draw samples and extract covariate data. This is by design.
Selecting background samples, computing sample weights, splitting train/test data, and specifying training parameters are all critical modeling choices that have profound effects on inference and interpretation.
The extra flexibility provided by `elapid` enables more control over the seemingly black-box approach of Maxent, enabling users to better tune and evaluate their models.
---
## How to cite
BibTeX:
```
@article{
Anderson2023,
title = {elapid: Species distribution modeling tools for Python}, journal = {Journal of Open Source Software}
author = {Christopher B. Anderson},
doi = {10.21105/joss.04930},
url = {https://doi.org/10.21105/joss.04930},
year = {2023},
publisher = {The Open Journal},
volume = {8},
number = {84},
pages = {4930},
}
```
Or click "Cite this repository" on the [GitHub page](https://github.com/earth-chris/elapid).
---
## Developed by
[Christopher Anderson](https://cbanderson.info)[^1] [^2]
[home-maxent]: https://biodiversityinformatics.amnh.org/open_source/maxent/
[r-maxnet]: https://github.com/mrmaxent/maxnet
[^1]: [Earth Observation Lab, Planet Labs PBC](https://www.planet.com)
[^2]: [Center for Conservation Biology, Stanford University](https://ccb.stanford.edu)