Wallace

a flexible platform for reproducible modeling of species niches and distributions

About

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.

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 repository or the Google Group forum (links above).

Resources

Publications

If you use Wallace in your research, please cite these papers.
Our latest software note is in Ecography, detailing the updates made in version 2, or see our initial publication in Methods in Ecology and Evolution for more information.

Kass JM, Pinilla-Buitrago GE, Paz A, Johnson BA, Grisales-Betancur V, Meenan SI, Attali D, Broennimann O, Galante PJ, Maitner BS, Owens HL, Varela S, Aiello-Lammens ME, Merow C, Blair ME, Anderson RP. (2023). wallace 2: a shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions. Ecography, Volume 2023(3), e06547. https://doi.org/10.1111/ecog.06547

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

Tutorials and Vignettes

For a tutorial, please see our updated vignette for version 2.0.0+. This vignette has lots of images, which makes the file size too big for CRAN, so we are hosting it here instead. This vignette is also available in Spanish.
You can also find the previous vignette (written for Wallace v1.0.5) here.

We also have a Module Addition Vignette for instructions on how to add your own module into the Wallace workflow.

Docker Image and Tools for Cloud Implementations

Wallace is available as a Docker image on Docker Hub (currently ver 1.1). Anyone who has Docker installed on their system can use this image to run Wallace without the need to interface with R. Follow these steps:

Check that Docker is running on your system
At a command line, run the following command: 'docker pull mlammens/wallace_v1:PE.1.1'
Next, run the following command: 'docker run -d -p 8080:8080 mlammens/wallace_v1:PE.1.1'
Open a browser and navigate to 'localhost:8080'

Wallace can also run in the CyVerse Visual Interactive Computing Environment (VICE). We have developed a VICE App that is currently available by contacting Matt Aiello-Lammens at maiellolammens@pace.edu, and will be publically available soon.

Slide Presentations

A generic presentation slide deck for Wallace is available as a PDF or a editable Power Point file. We are providing these files under the Creative Commons - Attribution - Share Alike 4.0 license.

Webinars

Members of our team have delivered webinars about Wallace in English and Spanish. Citations and links are below. We also have a YouTube page with additional videos in multuple languages.

Spanish: The following webinars were part of the "Modelado de Distribuciones Potenciales" series, organized by Angela Cuervo:

Paz, A. 3 October 2023. “Wallace EcoMod: Nuevas funcionalidades para aplicaciones en conservación”. Seminarios 2023 - Wallace EcoMod. Watch on YouTube.
Anderson, R. P. 21 May 2018. "El software Wallace para modelar nichos y distribuciones: Un coche con motor R, volante de ratón y cerebro de humano." Broadcast from the City College of New York, City University of New York. Watch on YouTube.

English: The following webinar was the "37th Global Online Biodiversity Informatics Seminar" in the Biodiversity Informatics Training Curriculum organized by Town Peterson:

Kass, J. M. 9 May 2018. "WALLACE: A flexible platform for reproducible modeling of species niches and distributions built for community expansion." Broadcast from the City College of New York, City University of New York. Watch on YouTube.

Education and Outreach

We encourage the use of Wallace for teaching species distribution modeling techniques or biogeography principles more generally. In fact, we have used Wallace for this very purpose at workshops delivered to multiple audiences. Here is an example of a course delivered at the Student Conference on Conservation Science - NY.

If you use Wallace in your teaching, we would like to hear about your experiences. Please take a moment to complete the short survey - Wallace external workshop and curriculum survey.

Current Development Team

Jamie M. Kass (co-lead developer) received his PhD at CUNY Graduate Center and City College of New York, did a Postdoc at Okinawa Institute of Science and Technology, and currently is Associate Professor at Tohoku University.

Gonzalo E. Pinilla Buitrago (co-lead developer) received his PhD from the CUNY Graduate Center and City College of New York. He is currently a Postdoctoral Researcher at University of Connecticut.

Andrea Paz (developer) received her PhD at CUNY Graduate Center and City College of New York, did her postdoctoral research at the Crowther Lab in ETH Zürich, and is now Assistant Professor at Université de Montréal.

Bethany A. Johnson (co-developer) received her Master's in Biology from City College of New York and is currently a Visiting Scientist at the Center for Biodiversity & Conservation at the American Museum of Natural History.

Beth E. Gerstner (developer) received her PhD from Michigan State University, is a NASA FINESST Award winner, and a Wallace fellow. She currently works for Map of Life at the Center for Biodiversity and Global Change at Yale University.

Daniel Lopez Lozano (developer) is the Biodiversity Informatics Specialist at the Center for Biodiversity & Conservation at the American Museum of Natural History.

Valentina Grisales-Betancur (developer) completed her undergraduate degree at EAFIT University in Colombia and visited the Anderson lab at CCNY and Blair lab at AMNH.

Dean Attali (developer, consultant) is an R-Shiny developer and consultant with a MSc in Bioinformatics from the University of British Columbia.

Managers

Robert P. Anderson (lead manager, developer) is a Professor of Biology at City College of New York, CUNY.

Matthew E. Aiello-Lammens (co-manager, developer) is an Associate Professor of Biology at Pace University.

Cory Merow (co-manager, developer) is currently a faculty researcher at the University of Connecticut.

Mary E. Blair (co-manager) is the Director of Biodiversity Informatics Research at the Center for Biodiversity and Conservation at the American Museum of Natural History.

Contributors

Sarah Meenan (contributor) completed her undergraduate degree from the City College of New York and now works for the NYC Parks Department.

Olivier Broennimann (contributor, external partner) is a staff scientist in the Department of Ecology and Evolution at University of Lausanne.

Peter J. Galante (contributor) was a Biodiversity Informatics Scientist at the Center for Biodiversity and Conservation at the American Museum of Natural History and now works as a Project Manager for Storke, LLC, a renewable energy company.

Brian S. Maitner (contributor, external partner) is a researcher at the Geography Department of the University at Buffalo, SUNY.

Hannah Owens (contributor, external partner) is an assistant professor at the Center for Global Mountain Biodiversity & the Center for Macroecology, Evolution, and Climate; Section for Biodiversity; Globe Institute; at the University of Copenhagen.

Sara Varela (contributor, external partner) is a Principal Investigator at the MAPAS Lab at the University of Vigo in Spain.

Past Developers

Bruno Vilela (co-developer) is a Professor of Spatial Ecology at the Federal University of Bahia (Salvador - Brazil).

Robert Muscarella (past co-developer) is Associate Professor in the Department of Ecology and Genetics at Uppsala University, Sweden.

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), DBI-1661510 (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.

This material is also based upon work supported by NASA under award No. 80NSSCK0406 (PI - Dr. Mary Blair at the American Museum of Natural History. More information on this portion of the project can be found at the maskRanger R package website. 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 Aeronautics and Space Administration.

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.

Mahmoud Shahin designed the WallaceEcoMod logo with inspiration from “Wallace’s butterfly” (Ornithoptera croesus; Wallace’s golden birdwing), an idea first suggested by Samuel Chang.