Seminar Notes

Leo Polansky Seminar

(all notes cover published results only)

  • Wavelet analysis does a nice trick of seeing frequency-domain spectra change over time, rather than being entirely in frequency space or entirely in time space.
  • higher rank elephants decrease their movement more in dry, resource-poor season than low rank. Guarding the good territory? I wonder if this is a stochastic effect - asset protection, where you take more risk when you have low assets than when you have higher assets, a feature that would dissappear in a deterministic environment.
  • Nice hidden markov model analysis from the mhsmm package.
  • movement time series – high impact public data or closely guarded secret? (top secret)

Michael Bonsall

(Seminar to the Mangel megagroup meeting)

  • uncertainty and variability in population dynamics. Mike uses the very words I’ve used to describe my interests: dynamic, nonlinear, and noisy.

Blasocyst Dynamics

  • Development of mammalian blastocyst much more messy/complicated than development in other taxa. heterogeneity in timing
  • Begins with ODE model with time lags (to avoid poisson waiting times). Then add a distribution over the time lag.
  • Invasion analysis of cell types differing in time. Widening distribution of time lags increases fitness. Interesting! But intuition/mechanism unclear
  • Now add process noise, observation error and priors on parameters to compare model to data. Variability can be explained entirely by differences in rates. (as estimated from a particle filter). Identifiability?

Bruchid Dynamics

  • Spatial dynamics with beatles and their parasitic wasps.
  • Beautiful microcosm setup that follows Nicholson-Bailey dynamics.
  • Within patch dynamics show regimes.
  • Consider stochastic birth-death-diffusion model
  • Stochastic focusing / demographic heterogeneity observed

Bipolar disorder dynamics

  • (Inductive example)
  • EM algorithm for missing values in time lag model

Other activities today

  • working on nominations
  • ropensci sustainability plan (see email threads),
  • also see the Conceptualizing an Institute for Sustainable Earth and Environmental Software (ISEES), https://isees.nceas.ucsb.edu/
  • friendly review phylolm package and preprint
  • summarizing reimbursement form
  • updated issues lists for notebook
  • Bonsall speaker dinner

Further reading

Following up on discussions today, seemed like a good time to reread:

  • Bonsall, M. B. & Hastings, A. 2004 Demographic and environmental stochasticity in predator - prey metapopulation dynamics. , 1043-1055. (doi:10.1111/j.0021-8790.2004.00874.x)

Also taking a look at the ‘stochastic focusing’ literature. Unclear if the term has caught on much beyond Paulsson and co. though.

  • Paulsson, J., Berg, O. G. & Ehrenberg, M. 2000 Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation. Proceedings of the National Academy of Sciences of the United States of America 97, 7148-53. (doi:10.1073/pnas.110057697)