Wallace

a flexible platform for reproducible modeling of species niches and distributions





Wallace is a modular, R-based platform for reproducible modeling of species niches and distributions. The application guides users through a complete analysis, from the acquisition of data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface.

Please read our new paper in Methods in Ecology and Evolution for more details.

Kass JM, Vilela B, Aiello‐Lammens ME, Muscarella R, Merow C, Anderson RP. (2018). Wallace: A flexible platform for reproducible modeling of species niches and distributions built for community expansion. Methods in Ecology and Evolution. 9:1151–1156. https://doi.org/10.1111/2041-210X.12945

For a tutorial, please see our new vignette for version 1.0.5. This vignette has lots of images, which makes the file size too big for CRAN, so we are hosting it here instead.

Wallace is open: the code is free to use and modify (GPL 3.0), and it gives users access to some of the largest public online biodiversity databases. The application is expandible, as users can author and contribute modules that enable new methodogical options. There are flexible options for user uploads and downloads of results. The session is interactive, with an embedded zoomable map, sortable tables, and assorted visualizations of results. Wallace is instructive, with guidance text throughout that educates users about theoretical and analytical aspects of each step in the workflow. Lastly, it is reproducible, as users can download an R Markdown file that reruns the analysis.

Wallace is written using the web app development R package shiny. Development requests or contributions should be directed to either the Github repo or the Google Group forum (links above).

A brief vignette outlining how to construct and add modules was presented at the 8th Biennial Conference of the International Biogeography Society in January 2017, during a workshop entitled "Integrating and cleaning biodiversity data: Workflows to model ranges and merge associated ecological, phylogenetic, and trait information" led by Dr. Cory Merow.


Dev Team

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Jamie M. Kass
Lead developer. is a PhD candidate at CUNY Graduate Center and City College of New York.
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Bruno Vilela
Bruno Vilela (co-developer) is a post-doctoral researcher at Washington University in St. Louis.
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Matthew E. Aiello-Lammens
Matthew Aiello-Lammens (co-developer) is Assistant Professor of Environmental Studies and Science at Pace University.
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Robert Muscarella
Robert Muscarella (co-developer) is a National Science Foundation post-doctoral fellow at Aarhus University in Denmark.
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Cory Merow
Cory Merow (co-developer) is a Research Scientist at Yale University (photo not shown).
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Robert P. Anderson
Robert P. Anderson (co-developer) is Professor of Biology at City College of New York, CUNY.


Acknowledgments


Wallace was recognized as a finalist for the 2015 Ebbe Nielsen Challenge of the Global Biodiversity Information Facility (GBIF), and received prize funding.

This material is based upon work supported by the National Science Foundation under Grant Numbers DBI-1650241 (RPA), DEB-1119915 (RPA), DEB-1046328 (MEA), and DBI-1401312 (RM). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Additional sources of funding for JMK include a CUNY Science Scholarship and a CUNY Graduate Center Provost Digital Innovation Grant, and for BV include a Coordination for the Improvement of Higher Education Personnel (CAPES) doctoral grant from Brazil.