Mbi Day Five Notes

Panel discussion

  • Hugh’s question on the usefulness of dynamic vs static models: do we have dynamical systems envy?
  • Chris: are temporal dynamics historical artefact, and space the new frontier?
  • Hugh: though decision theory is fundamentally temporal. really question of sequential decision vs single decision
  • Hugh, on what would be his priority if he had time for new question: Solve the 2 player, 2 step SDP competition closed form.
  • Paul: the narrow definitions of “math biology” with 1980s flavor.
  • @mathbiopaul: Formulating the hard problems arising in application in an appropriate abstraction that mathematicians will attack.
  • Leah raises issue of publishing software and reproducibility
  • Julia mentions Environmental modeling and software journal

Notes from some discussions today


Trying to understand pattern of increasing ENPV with increasing stochasticity. Despite having the same optimal policy inferred under increasing stochasticity (i.e. still in Reed’s self-sustaining criterion, below \(\sigma_g\) of 0.2 or so) the average over simulated replicates is higher. We don’t seem to obtain the theoretical ENPV, but something less, in either case. See code noise_effects.md.


Schema.org defines a vocabulary for datasets (microdata/rdfa)

Rutger gives a one-liner solution for tolweb to nexml using bio-phylo perl library:

perl -MBio::Phylo::IO=parse -e 'print parse->to_xml' format tolweb as_project 1 url 'https://tolweb.org/onlinecontributors/app?service=external&page=xml/TreeStructureService&node_id=52643'

Hmm, there’s a journal of Ecological Informatics.


  • Rebecca S. Epanchin-Niell, Robert G. Haight, Ludek Berec, John M. Kean, Andrew M. Liebhold, Helen Regan, (2012) Optimal Surveillance And Eradication of Invasive Species in Heterogeneous Landscapes. Ecology Letters 15 803-812 10.1111/j.1461-0248.2012.01800.x
  • Rebecca S. Epanchin-Niell, James E. Wilen, (2012) Optimal Spatial Control of Biological Invasions. Journal of Environmental Economics And Management 63 260-270 10.1016/j.jeem.2011.10.003
  • J. Esper, U. Buntgen, D. C Frank, D. Nievergelt, A. Liebhold, (2007) 1200 Years of Regular Outbreaks in Alpine Insects. Proceedings of The Royal Society B: Biological Sciences 274 671-679 10.1098/rspb.2006.0191
  • unknown Fagan, unknown Meir, unknown Prendergast, unknown Folarin, unknown Karieva, (2001) Characterizing Population Vulnerability For 758 Species. Ecology Letters 4 132-138 10.1046/j.1461-0248.2001.00206.x
  • A. R. Hall, A. D. Miller, H. C. Leggett, S. H. Roxburgh, A. Buckling, K. Shea, (2012) Diversity-Disturbance Relationships: Frequency And Intensity Interact. Biology Letters 8 768-771 10.1098/rsbl.2012.0282
  • Elizabeth Eli Holmes, John L. Sabo, Steven Vincent Viscido, William Fredric Fagan, (2007) A Statistical Approach to Quasi-Extinction Forecasting. Ecology Letters 10 1182-1198 10.1111/j.1461-0248.2007.01105.x
  • Brian Leung, Nuria Roura-Pascual, Sven Bacher, Jaakko Heikkilä, Lluis Brotons, Mark A. Burgman, Katharina Dehnen-Schmutz, Franz Essl, Philip E. Hulme, David M. Richardson, Daniel Sol, Montserrat Vilà, Marcel Rejmanek, (2012) Teasing Apart Alien Species Risk Assessments: A Framework For Best Practices. Ecology Letters 15 1475-1493 10.1111/ele.12003
  • A. D. Miller, S. H. Roxburgh, K. Shea, (2011) How Frequency And Intensity Shape Diversity-Disturbance Relationships. Proceedings of The National Academy of Sciences 108 5643-5648 10.1073/pnas.1018594108
  • Adam David Miller, Stephen H. Roxburgh, Katriona Shea, (2011) Timing of Disturbance Alters Competitive Outcomes And Mechanisms of Coexistence in an Annual Plant Model. Theoretical Ecology 5 419-432 10.1007/s12080-011-0133-1