Simple SDM Layers in Julia

The SimpleSDMLayers provides an interface to facilitate the manipulation of raster data for species distributions modeling in Julia.

The two core types of the package are SimpleSDMPredictor and SimpleSDMResponse. The only difference between the two is that predictors are immutable, but responses are. All types belong to the abstract SimpleSDMLayer, and are organised in the same way: a grid field storing a matrix of data (of any type!), and the left, right, bottom, and top coordinates (as floating point values). Of course these details are largely irrelevant, since we have overloaded a large number of methods from Base, to make indexing, converting, and modifying data as easy as possible.

The aim of the package is to deliver (i) a series of methods to manipulate raster data, and (ii) facilitated access to common datasets used to train species distribution models. Despite what the name may suggest, this package does not implement SDMs, but is instead intended as a library usable for this purpose. Nevertheless, the documentation contains a few example of building models, and integrating this package with the GBIF API.

The documentations is split in three sections. The manual is a fairly exhaustive documentation of the functions, methods, types, and interfaces, and it is a good idea to skim it first, and come back for a focused reading when you have a specific use-case in mind. The general examples section is a collection of mostly disconnected workflows, intended to show how SimpleSDMLayers interacts with other packages. It should give you a better understanding of you can actually use the package.

Finally, the SDM case studies are a more linear series of vignettes, covering occurrence data, variable selection, bulding a presence-only model, generating pseudo-absences, and using a machine learning approach to do range forecasting under climate change. This last section can be used as a template to develop new analyses, and will use almost all the features in the package. All of the SDM vignettes use the same species throughout - Hypomyces lactifluorum is a fungus of moderate commerical importance in North America, whose distribution is probably going to be affected by climate change.