Complex Systems Summer School 2017-Tutorials

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Complex Systems Summer School 2017

Nonlinear Time Series Analysis using Empirical Dynamic Modeling (EDM)

Hey all, I've done some work with non-linear time series analysis using empirical dynamic modeling (Sugihara et al., 2012). If anyone is interested in these approaches, I'd be happy to give a tutorial on the R EDM package that can be used to look for 1. nonlinearity in time-series, 2. causality between variables, and 3. optimizing combinations of system variables to create "equation-free mechanistic models". I've used this method looking at marine phytoplankton time-series, combining several species and environmental variables. The final product was messy, but helped identify important system variables in ecosystems :)


Online walk-through of the R EDM package [1]!

  • Sugihara, George et al. “Detecting Causality in Complex Ecosystems.” Science 338.6106 (2012): 496–500. Web.
  • Ye, Hao et al. “Equation-Free Mechanistic Ecosystem Forecasting Using Empirical Dynamic Modeling.” Proceedings of the National Academy of Sciences 112.13 (2015): E1569–E1576. Web.

Interested Participants:

  • Zhiya Zuo. Thanks for this! Is there a desired time/location?
--> No plan for a time/location yet...I'm waiting to see if there is enough interest. I would be happy to do this whenever.
  • Kayla Sale
  • Jake Weissman
  • Ximo Pechuan
  • Markus Junginger
  • Alicia Kraay
  • Kyle Lemoi
  • Anand Nair
  • Carla Rivera
  • Ramona Roller
  • Tim Kunisky
  • Marco Pangallo
  • Hilje Doekes
  • Spencer Fox
  • Shanee Stopnitzky - I wrote a little condensed version of a tutorial for this package that I can send around
  • Shing Zhan
  • Katarina Mayer
  • Rachel Gicquelais
  • Elaine Bochniewicz
  • Mark
  • Stefan

Chemical Reaction Network Theory

Network Analysis with Python - igraph

Hi guys, Today I'm gonna give a quick tutorial on network analysis with Python. My library of choice is igraph because it's a good balance between performance and simplicity compared to other libraries. Thu Jun 22 - 7pm - lecture hall Since the library has some dependencies, I recommend you installing Docker

Once you have it installed and running, we're going to use a docker container I created for network analysis. You'll have to run the two commands bellow from the terminal/prompt.

docker pull hsbarbosa/network-science

docker run -ti -p 8888:8888 -v "$PWD":/home/me hsbarbosa/network-science