Other stuff from the lab

On occasion, we produce something that might be useful to others. A few of these items are collected here.


Portfolio is a decision support tool for assembling systems of nature reserves. The tool uses variations on greedy heuristic algorithms applied to multiple decision criteria: patch area, habitat quality, species richness and rarity, and connectivity measures based in graph theory. The program is interactive, and at each iteration it quantifies the implications of choosing a particular patch on the relative value of all other patches. Its aim is to illustrate the consequences of user decisions to value one criteria (e.g., species rarity) over another (e.g., connectivity). In this way, the tool informs decisions without actually forcing any particular decision.

You can download a package of stuff here: portfolio.zip. This includes an old DOS version, a spiffy Windows version coded by Jason Roberts, help files, and some demo data. You should cite the program by referencing the book chapter that demonstrates its use as a teaching tool:

Urban, D.L. 2002. Prioritizing reserves for acquisition. Pages 293-305 in S.E. Gergel and M.G. Turner (eds.), Learning landscape ecology: a practical guide to concepts and techniques. Springer-Verlag, New York.

The ecodist package for R

Package ecodist is a library of functions to conduct statistical analyses based on ecological dissimilarities or distances, packaged for use in the R computing environment. Analyses include nonmetric multidimensional scaling, principal coordinates analyses, simple and partial Mantel tests, and a variety of support functions. Sarah Goslee began working on the ecodist package while a student here; she continues to support it.

You can download the package from the R download site: CRAN. The preferred citation is:

Goslee, S.C., and D.L. Urban. 2007. The ecodist package for dissimilarity-based analyses of ecological data. J. Statistical Software 22:7.

ArcGIS Toolboxes for habitat analysis and connectivity

We are at beta-release stage (almost!) for a set of toolboxes for use in ArcGIS. The tools support a variety of tasks for conservation planning at the landscape scale, with a special focus on characterizing habitat patches in terms of geometry, biodiversity support potential, and connectivity (based on graph theory).

We will publish the tools here when they are ready.