Capstone Beginnings

1 month into my summer vacation, and I have been spending time doing research on ecological modelling, wrapping up work at Code Gakko and doing a side project on scraping and representing MOE data. With 2 more months left, I have decided to start a series on my capstone topic, so that I may document the research I’m doing, and make it more robust. From time to time, I will also put up my thoughts regarding Code Gakko as well as my side project as and when I make some progress.

So, *drumrolls*


The most important question out there, that Maurice asked me:

What do you want to learn?

After all, the capstone is a 10MC subject.

Choose one approach, master it.

After much thought, I want to learn 2 things:

  1. To know how agent-based models work, what their limitations are, and finding out if there is a scientific way of going about working with ABMs
  2. How to create a webapp for this model, for educational and research purposes

Capstone Beginnings

So far, this is what I have, just a little plan that outlines the knowledge I require to do my capstone. One advice I received from my advisor Professor Gastner is that many students don’t do their literature review. What is the literature review anyway? It is a process by which you look at all the related work that has been done out there, and knowing how your work is situated in the greater literature of academic research.

In my context, I am doing an ecological model that simulates tropical forests for chronosequences of more than 100 years. I am investigating how the biodiversity of a landscape can be affected by different parameters, such as dispersal limitation, functional traits of species etc.

Thus the relevant questions / content I need to look out for are as such:

  1. Why is biodiversity important?
  2. What are current measures of biodiversity?
  3. What are the theoretical factors that affect biodiversity?
  4. Why is there a need for a model in the first place?
  5. What assumptions am I making in my model?
  6. How do I choose the parameters for my model?
  7. Is there a mathematical basis for the model?

I have sought out a few resources to kickstart this research process and they are as follows:

Concepts of Biodiversity / Community Ecology:

  1. Colwell, R. K. (2009). Biodiversity: concepts, patterns, and measurement. The Princeton Guide to Ecology, 257–263.
  2. Cernansky, R. (2017). Biodiversity moves beyond counting species. Nature News, 546(7656), 22.
  3. Verhoef, H. A., & Morin, P. J. (Eds.). (2010). Community ecology: processes, models, and applications. Oxford: Oxford University Press.

Concepts of Ecological Modeling / Statistics:

  1. Kéry, M., & Schaub, M. (2012). Brief Introduction to Bayesian Statistical Modeling. In Bayesian Population Analysis using WinBUGS (pp. 23–45). Elsevier. Retrieved from
  2. Semeniuk, C. A., Musiani, M., & Marceau, D. J. (2011). Integrating spatial behavioral ecology in agent-based models for species conservation. Edited by Adriano Sofo, 1.
  3. Grant, W. E., & Swannack, T. M. (2008). Ecological modeling: a common-sense approach to theory and practice. Malden, MA ; Oxford: Blackwell Pub.
  4. Gimblett, H. R. (Ed.). (2002). Integrating geographic information systems and agent-based modeling techniques for simulating social and ecological processes. Oxford ; New York: Oxford University Press.
  5. Botkin, D. B. (1993). Forest dynamics: an ecological model. Oxford ; New York: Oxford University Press.
  6. Jørgensen, S. E., & Bendoricchio, G. (2001). Fundamentals of ecological modelling (3rd ed). Amsterdam ; New York: Elsevier.

More thoughts to come!




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