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 repo or the Google Group forum (links above).
Have a look at our 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.
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.
Members of our team have delivered webinars about Wallace in English and Spanish. Citations and links are below.
Spanish: The following webinar was part of the "Modelado de Distribuciones Potenciales" series, organized by Angela Cuervo:
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.
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.
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.