Manual

SpeciesDistributionToolkit.jl is a collection of packages for species distribution modeling and biodiversity research, for the Julia programming language.

Not just for research!

This package is now used in pipelines in BON in a Box, GEOBON's project to automate the calculation and representation of the post-2020 GBF indicators.

Contents of the package

The package offers a series of methods to acces data required to build species distribution models, including:

• a wrapper around the GBIF occurrences API to access occurrence data

• a wrapper around the Phylopic images API

• ways to generate fake occurrences with statistical properties similar to actual occurrences

• ways to generate pseudo-absences based on a series of heuristics

• a simple way to represent layers as mutable objectcs

• utility functions for teaching species distribution models

• a way to collect historic and future climate and land-use data to feed into the models, pre-loaded with datasets like CHELSA, WorldClim, EarthEnv, PaleoClim, etc

• an interface to Makie for plotting and data visualisation

Installation

The only package you need to install is SpeciesDistributionToolkit itself, which can be done using

import Pkg
Pkg.add("SpeciesDistributionToolkit") 

This will automatically install all the sub-packages.

Contents of the manual

This manual is split into two sections: tutorials, which are medium to long examples of using the full functionality of the package; and how-tos, which are shorter (and denser) summaries of how to achieve a specific task.

Current component packages

The packages do work independently, but they are designed to work together. In particular, when installing SpeciesDistributionToolkit, you get access to all the functions and types exported by the component packages. This is the recommended way to interact with the packages.

Access to GBIF data

GBIF.jl is a wrapper around the GBIF API, to retrieve taxa and occurrence datasets, and perform filtering on these occurrence data based on flags.

Handling occurrence data

OccurrencesInterface.jl is a lightweight, general purpose interface that allows other types to be used with the Species Distribution Toolkit package.

Downloading and managing environmental data

SimpleSDMDatasets.jl is an efficient and transparent, interface-based way to download and store environmental raster data for consumption by other packages.

Manipulating raster

SimpleSDMLayers.jl offers a series of types and common operations on raster data.

Simulating occurrence data

Fauxcurrences.jl is a package to simulate realistic species occurrence data from a known series of occurrences, with additional statistical constraints.

Access to the Phylopic library

Phylopic.jl is a wrapper around the Phylopic API.

Tools for workshops and education

SDeMo.jl is a series of very simple SDMs and utility functions for education, with some tools for interpretable machine learning.