Wallace: A flexible platform for reproducible modeling of species
niches and distributions built for community expansion
Jamie M. Kass, Bruno Vilela, Matthew E. Aiello-Lammens, Robert Muscarella, Cory
Merow & Robert P. Anderson …
… and Jenna Rios, Sara Varela, Hannah L., Owens, Brian S. Maintner, Olivier
Broennimann, Mary E. Blair, Ned Horning, Jorge Velásquez-Tibatá, Gonzalo E. PinillaBuitrago, Beth E. Gerstner, Peter J. Galante, Sarah I. Meenan, Valentina GrisalesBetancur, Cecina Babich-Morrow, Erica E. Johnson …

…
and many collaborating institutions!

Wallace v1 overview presentation, CC BY SA license, 10 December 2018

Range estimates neededApplied biodiversity informatics
Anderson (2012)

Agenda: Making data and modeling ready to addresscritical environmental issues of the 21st century

Agenda: applied biodiversity informatics

1. High-quality data, ready to be accessed when theparticular problem presents itself
2. Software that achieves an appropriate balance
between automation and supervision
3. Scientists capable of building, applying, andappraising high-quality models

Correlative modeling of species niches and rangesOccurrence
records
Algorithm
Environmental
data

Modelof niche

SuitableareasCorrelative modeling of species niches and ranges

another place

Occurrence
records
Algorithm
Environmental
data

Modelof niche

Suitableareas

another time

Conservation, invasive species, zoonotic diseases,
climate change

Anderson (2015)

Agenda: applied biodiversity informatics
Anderson (2012)

Software that achieves an appropriate balance
between automation and supervision• automates repetitive aspects• forces user to make critical biological andconceptual decisions• general with respect to algorithms usedProblems with existing analyses
Existing GUIs
- (too) easy
- default settings- inflexible- infrequently updated- strings of applications

Problems with existing analyses
Existing GUIs
- (too) easy
- default settings- inflexible- infrequently updated- strings of applications
Code- error-prone- not easily generalizable- slow to be taken up

From R to a web app

Innovative use of GBIF
occurrence dataCombine code-based methods with GUI

Foreground:
Flexible, interactive,
expandable GUI

Background:R code from newpackages: reproducible

Wallace: currently under expansion …

Jamie M. Kass, Bruno Vilela, Matthew E. Aiello-Lammens, RobertMuscarella, Cory Merow & Robert P. Anderson… and Jenna Rios, Sara Varela, Hannah L., Owens, Brian S.
Maintner, Olivier Broennimann, Mary E. Blair, Ned Horning, Jorge
Velásquez-Tibatá, Gonzalo E. Pinilla-Buitrago, Beth E. Gerstner, PeterJ. Galante, Sarah I. Meenan, Valentina Grisales-Betancur, Cecina
Babich-Morrow, Erica E. Johnson …

…

What is Wallace?

Point-and-click (GUI) application that includes moststeps of a niche/distribution modeling workflow• Harnesses R packages and gives credit to theirauthors

R packages on the inside… and now many other contributors

WallaceQualities of Wallace

Wallace’s code is freeand OPEN(& users can download
data from online
databases.)Qualities of Wallace
Wallace provides
GUIDANCE

that addresses
conceptual andmethodologicalissues.

Qualities of Wallace
Wallace is FLEXIBLE
by providing
multiple options,and allowing user
inputs anddownloads for mostcomponents.

Qualities of Wallace
Wallace features
INTERACTIVE

maps, tables, andgraphs to explore
data and modelpredictions.

Qualities of Wallace
Wallace isREPRODUCIBLE

by providing
executable code fordocumenting andrerunning theanalysis.

Qualities of Wallace
Wallace is EXPANDABLE!
by featuring different
methodological options(modules) that
researchers cancontribute to advancefunctionality.

Wallace: software for niche/distribution modeling

Qualities:

Female and minority-student coder-biologists

open
instructive
flexibleinteractive
reproducible
expandable
broadening
human diversity

External partners, undergraduates, and interns/fellows:Sara Varela, Hannah L. Owens, Cecina Babich-Morrow,
Jenna Rios, Sarah I. Meenan, Valentina Grisales-Betancur

Installing Wallace• Install R and (optionally) Rstudio• For Maxent java version, install maxent.jar(https://biodiversityinformatics.amnh.org/open_source/maxent/ and appropriate Java version for yoursystem, then place maxent.jar in dismo folder• Install the wallace package from CRAN

• Troubleshooting on Github page(https://github.com/wallaceEcoMod/wallace)Wallace today
1. Full Release 1.0.6 (Kass etal. 2018, Methods in Ecology &Evolution software note; Googlegroup; Wallace e-mail)NSF DEB-1119915& DBI-1650241

2. Ongoing NSF funding to workwith external partners to add
new modules
3. Ongoing NASA funding, led
by Mary Blair (AMNH), todevelop new R packages andadd them to Wallace andinterface with BioModelos

NSF DBI-1661510

Mary E. Blair

NASA 80NSSC18K0406

Acknowledgments

https://wallaceecomod.github.io/
http://www.andersonlab.ccny.cuny.edu

Anderson lab(chronosequence)