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Contemporary species distribution modeling tools for python.

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Source code: earth-chris/elapid

🐍 Introduction

elapid provides python support for species distribution modeling. This includes a custom implementation of Maxent and a suite of tools 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).

🌱 Installation

pip install elapid

This should suffice for most linux/mac users, as there are available unix builds of the underlying python dependencies (numpy, sklearn, glmnet, rasterio, etc.).

Windows installs are more challenging. glmnet has to compile some fortran code on install, meaning you need to have a fortran compiler running (like MinGW-w64 or Cygwin).

You can review Windows install instructions with slightly more detail, or contribute a better solution, at this issue.

🌳 Package design

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.

It does the following things reasonably well:

🌐 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_geoseries(), elapid.sample_raster(), or elapid.sample_bias_file()).

📈 Vector annotation

Annotate point data with coincident raster data, creating GeoDataFrames with sample locations and co-aligned covariate values (using elapid.annotate()).

📊 Zonal statistics

Calculate zonal statistics from multi-band, multi-raster data into a single GeoDataFrame from one command (using elapid.zonal_stats()).

🐛 Feature transformations

Transform covariate data into derivative features to expand data dimensionality (primarily the elapid.MaxentFeatureTransformer(), but see others under elapid.features)

🐦 Species distribution modeling

Train and apply generic species distribution models (like elapid.MaxentModel() and elapid.NicheEnvelopeModel()).

🌏 Applying models to rasters

Apply pixel-based models with a .predict() method to rasters (like training a RandomForestClassifier() and applying with elapid.apply_model_to_rasters()).

☁️ Cloud-native geo support

Work with cloud- or web-hosted raster/vector data (on https://, gs://, s3://, etc.).

🐍 elapid requires some effort on the user's part to draw samples and extract covariate data. This is by design. Selecting background samples, splitting train/test data, and specifying model parameters are all critical modeling choices that have profound effects on model prediction and interpretation. This extra flexibility provides more control over the seemingly black-box approach of Maxent's java implementation, and enabling users to better tune and evaluate their models.


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