GUI: A user-friendly interface for SSDM

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.

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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.

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Natural history records

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

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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

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Intermediate parameterization

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Advanced parameterization

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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

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Species-level results

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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.

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SSDM documentation built on Oct. 24, 2023, 5:08 p.m.