Wallace Ecological Modeling Application Vignette

Jamie M. Kass

Sarah I. Meenan

Gonzalo E. Pinilla-Buitrago

Cory Merow

Robert P. Anderson

06/08/2018; updated 07/12/18

Preface

This vignette was written for Wallace v. 1.0.5, so if you are using a different version, some things may not match up. Additionally, we anticipate that this vignette and any others in the wallace package will be updated regularly in accordance with ongoing development.

Introduction

Wallace is an R-based GUI application for ecological modeling that currently focuses on building, evaluating, and visualizing models of species niches and distributions. We will refer to these models as species distribution models (SDMs), and we will not explain them at length here—as you read through, you will be pointed to some sources of detailed info within the application for reference.

Wallace has many qualities which we think make it a good example of next-generation scientific software: it’s 1) open, 2) expandable, 3) flexible, 4) interactive, 5) instructive, and 6) reproducible. The application features a pannable/zoomable map and dynamic plots and tables. Data for the models can be downloaded from online databases or uploaded by the user. Most results can be downloaded, including the option to save R code that can reproduce your analysis. For more details, including on SDMs, please see our publication in Methods in Ecology and Evolution. The citation is below:

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.ezproxy.gc.cuny.edu/10.1111/2041-210X.12945

The Wallace project’s main page has links to the Google Group, the official email, the CRAN page hosting the stable version, and the Github development page.

Setup

For wallace to work, you should be using the latest version of R (or at least later than version 3.2.1). Download for Windows or Mac.

Let’s first install and load Wallace. Open either the base R software or RStudio and run the code below. It’s the only code you’ll have to run to use Wallace.

# install the package
install.packages('wallace')
# load the package
library(wallace)
# run the app
run_wallace()

The Wallace GUI will open in your default web browser and the R console will be occupied. You can exit Wallace by hitting Escape while in the R console, or by closing the browser window. A note: if you close the browser window running Wallace, your session will be over and all progress will be lost.

If you’d like to use the R console while running Wallace, open a terminal window (MacOS/Linux) or command prompt (Windows), initialize R, and then run the lines above. An example with Terminal in MacOS is below.