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### **What is *Wallace*?**  

Welcome to *Wallace*, a flexible application for reproducible ecological modeling, built for community expansion. The current version of *Wallace* (v1.0.5) steps the user through a full niche/distribution modeling analysis, from data acquisition to visualizing results.

The application is written in `R` with the web app development package `shiny`. Please find the stable version of *Wallace* on <a href="https://CRAN.R-project.org/package=wallace" target="_blank">CRAN</a>, and the development version on <a href="https://github.com/wallaceEcoMod/wallace" target="_blank">Github</a>. We also maintain a *Wallace* <a href="https://wallaceecomod.github.io/" target="_blank">website</a> that has some basic info, links, and will be updated with tutorial materials in the near future.

Please find a full <a href="https://wallaceecomod.github.io/vignettes/wallace_vignette.html" target="_blank">vignette</a> for *Wallace* on our website. This vignette has lots of images, which makes the file size too big for CRAN, so we are hosting it on the website instead. 

*Wallace* is designed to facilitate spatial biodiversity research, and currently concentrates on modeling species niches and distributions using occurrence datasets and environmental predictor variables. These models provide an estimate of the species’ response to environmental conditions, and can be used to generate maps that indicate suitable areas for the species (i.e. its potential geographic distribution; Guisan & Thuiller 2005; Elith & Leathwick 2009; Franklin 2010a; Peterson et al. 2011). This research area has grown tremendously over the past two decades, with applications to pressing environmental issues such as conservation biology (Franklin 2010b), invasive species (Ficetola et al. 2007), zoonotic diseases (González et al. 2010), and climate-change impacts (Kearney et al. 2010).

Also, for more detail, please see our paper in *Methods in Ecology and Evolution*.

Kass JM, Vilela B, Aiello-Lammens ME, Muscarella R, Merow C, Anderson RP. Wallace: A flexible platform for reproducible modeling of species niches and distributions built for community expansion. Methods Ecol Evol. 2018;00:1–6. https://doi.org/10.1111/2041-210X.12945

### **Who is *Wallace* for?**  

We engineered *Wallace* to be used by a broad audience that includes graduate students, ecologists, conservation practitioners, natural resource managers, educators, and programmers. Anyone, regardless of programming ability, can use *Wallace* to perform an analysis, learn about the methods, and share the results. Additionally, those who want to disseminate a technique can author a module for *Wallace*. 

### **Attributes of _Wallace_**

* **<span style="color:blue">open</span>**: 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

* **<span style="color:blue">expandible</span>**: users can author and contribute modules that enable new methodogical options

* **<span style="color:blue">flexible</span>**: options for user uploads and downloads of results

* **<span style="color:blue">interactive</span>**: includes an embedded zoomable `leaflet` map, sortable `DF` data tables, and visualizations of results

* **<span style="color:blue">instructive</span>**: features guidance text that educates users about theoretical and analytical aspects of each step in the workflow

* **<span style="color:blue">reproducible</span>**: users can download an `rmarkdown` .Rmd file that when run reproduces the analysis

### **Contribute to _Wallace_**

Contributors should submit pull requests to the *Wallace* <a href="https://github.com/wallaceEcoMod/wallace" target="_blank">Github account</a> for module authorship or significant code contributions to either the UI or server files. Also, please connect on Github to post code-related issues and the <a href="https://groups.google.com/forum/#!forum/wallaceecomod" target="_blank">Google Group</a> for methodological and other broader-scope questions, thoughts, or suggestions for improvement.

### **Contact us**

Please <a href="mailto:wallaceecomod@gmail.com">email us</a> with any other questions.

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#### **Acknowledgments**

We dedicate this software to Alfred Russel Wallace, the co-discoverer of evolution by natural selection and the founder of the field of biogeography.

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#### **References**

1. Elith J. & Leathwick J.R. (2009). Species distribution models: ecological explanation and prediction across space and time. *Annual Review of Ecology, Evolution, and Systematics*. 40: 677–697.

2. Ficetola G.F., Thuiller W. & Miaud C. (2007) Prediction and validation of the potential global distribution of a problematic alien invasive species—the American bullfrog. *Diversity and Distributions*, 13, 476-485.

3. Franklin J. (2010a). Mapping species distributions: spatial inference and prediction. Cambridge: Cambridge University Press.

4. Franklin J. (2010b) Moving beyond static species distribution models in support of conservation biogeography. *Diversity and Distributions*, 16, 321-330.

5. González, C., Wang, O., Strutz, S. E., González-Salazar, C., Sánchez-Cordero, V., & Sarkar, S. 2010. Climate change and risk of leishmaniasis in North America: predictions from ecological niche models of vector and reservoir species. *PLoS Neglected Tropical Diseases*, 4:e585.

6. Guisan A. & Thuiller W. (2005). Predicting species distribution: offering more than simple habitat models. *Ecology Letters*. 8: 993–1009.

7. Kearney M.R., Wintle B.A. & Porter W.P. (2010) Correlative and mechanistic models of species distribution provide congruent forecasts under climate change. *Conservation Letters*, 3, 203-213.

8. Peterson A.T., Soberón J., Pearson R.G., Anderson R.P., Martinez-Meyer E., Nakamura M., Araújo M.B. (2011). Ecological niches and geographic distributions. Princeton, New Jersey: Monographs in Population Biology, 49. Princeton University Press.
