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The package ‘SSDM’ offers a user-friendly interface built with the web application framework for R Shiny. The graphical user interface is launched with the function gui.

The interface has three tabs on the left, appearring successively: Load to load datasets or previous models and preview the data, Modelling to specify, train/test and save models, and Results to view the results and compare the performances.

Data inputs

The Load tab allows to load a new dataset or a previously saved model. Pop-up windows for data selection contains a link toward example raw data in the drop down menu.

Environmental variables

Top-left panel allows to load environmental variables through rasters. Don’t forget to specify which variable should be considered as a categorical variable.

Natural history records

Second panel allows to load occurrences through csv or txt files. Don’t forget to specify raw data formatting.

Model

The Modelling tab proposes three types of models: individual species distribution model (SDM), ensemble species distribution model (ESDM), or stacked species distribution model (SSDM). The Modelling tab contains three sub-tabs offering different levels of parameterization according to the user’s level of expertise: (1) Basic to select the model algorithm(s), the number of runs per model algorithm, the model evaluation metric(s), and the methods to be used to map diversity and endemism; (2) Intermediate to set pseudo-absence selection (number and strategy), the cross-validation method, the metric used to estimate the relative contribution of environmental variables, the ESDM consensus method, and the SSDM stacking method; and (3) Advanced to set algorithm parameters.

Basic parameterization

Intermediate parameterization

Advanced parameterization

Results

The Results tab gives maps and graphs summurizing the results at stack and species levels: model maps (species habitat suitability, species richness and endemism), relative contribution of environmental variables, model accuracy assessment, and between-algorithms correlation.

Stack-level results

Species-level results

Save

The interface includes a panel to save result maps in GeoTIFF format (.tif) compatible with most GIS softwares, and other numerical results as comma separated values (.csv) files.

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.
Health stats visible at Monitor.