SSDM {SSDM}

SSDM: Stacked species distribution modelling

Description

SSDM is a package to map species richness and endemism based on Stacked Species Distribution Models (SSDM). It provides tools to build SDM, i.e. a single species fitted with a single algorithm, Ensemble SDM (ESDM), i.e. a single species fitted with multiple algorithms, SSDM several species with one or more algorithms. The package includes numerous modelling algorithms, and specifiable ensemble aggregating and stacking methods. This package also provides tools to evaluate and explore models such as variable importance, algorithm accuracy, and between-algorithm correlation, and tools to map results such as habitat suitability maps, binary maps, between-algorithm variance maps. For ease of use, the SSDM package provides a user-friendly graphical interface (gui).

Details

The SSDM package provides five categories of functions (that you can find in details below): Data preparation, Modelling main functions, Model main methods, Model classes, and Miscellaneous.

Data preparation

load_occ

Load occurrence data

load_var

Load environmental variables

Modelling main functions

modelling

Build an SDM using a single algorithm

ensemble_modelling

Build an SDM that assembles multiple algorithms

stack_modelling

Build an SSDMs that assembles multiple algorithms and species

Model main methods

ensemble,Algorithm.SDM-method

Build an ensemble SDM

stacking,Ensemble.SDM-method

Build an SSDM

update,Stacked.SDM-method

Update a previous SSDM with new occurrence data

Model classes

Algorithm.SDM

S4 class to represent SDMs

Ensemble.SDM

S4 class to represent ensemble SDMs

Stacked.SDM

S4 class to represent SSDMs

Miscellaneous

gui

User-friendly interface for SSDM package

plot.model

Plot SDMs

save.model

Save SDMs

load.model

Load SDMs