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This repository contains an R package that implements Species Distribution Modeling methods which work even when there are relatively few occurrence records (as is the case for poorly-sample or range-restricted species). These methods were primarily developed by the Drake lab, and include three types of methods: 1) Plug-and-play models, 2) environmental-range models, and 3) density-ratio models. Most of the important functions in this package are wrappers around existing functions that handle density estimation or density-ratio estimation. Much of this code was created by modifying existing code at https://github.com/DrakeLab/PlugNPlay in order to make functions more modular and extensible.
The package is build on a hierarchy of modular functions, each of which calls on lower-level functions:
make_range_map and
evaluate_range_map, which are wrappers for…fit_plug_and_play,
fit_density_ratio, project_plug_and_play, and
project_density_ratio, which are wrappers for …pnp_kde or
dr_ulsif. These modules both model the environmental
covariates and predict values at environmental covariates from fitted
models. These modules are largely wrappers around existing functions for
fitting density functions or density-ratios. Modules beginning with
“pnp_” pertain to density functions while models beginning with “dr_”
pertain to density ratio functions.This hierarchical structure built on low-level internal modules is designed to allow for the easy addition of new methods by adding small, self-contained modules. The highest-level functions are intended only for quick-and-dirty analyses or quick visualizations. We recommend that users focus on the “fit” and “project” functions for work intended for publication.
In general usage, the term plug-and-play (PNP) refers to software or hardware that can be connected without any additional setup or configuration. In the context of species distribution models, plug-and-play is a framework developed by Drake and Richards (https://esajournals.onlinelibrary.wiley.com/doi/full/10.1002/ecs2.2373) that recognizes that species distribution models can be constructed by “plugging in” any methods that can estimate density functions.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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