GUI: A user-friendly interface for SSDM
2023-10-24
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.
